From b2a384e830227b7f701ff7da985cb8e934375f8d Mon Sep 17 00:00:00 2001 From: Riley-Grindle Date: Thu, 3 Oct 2024 16:23:55 +0000 Subject: [PATCH] params.genome default to null (boilerplate config opt) --- hash.txt | 2746 --------------------------------------- lib/WorkflowMain.groovy | 12 +- nextflow.config | 1 + 3 files changed, 2 insertions(+), 2757 deletions(-) delete mode 100644 hash.txt diff --git a/hash.txt b/hash.txt deleted file mode 100644 index e5960fd..0000000 --- a/hash.txt +++ /dev/null @@ -1,2746 +0,0 @@ - - N E X T F L O W ~ version 24.04.4 - -Launching `main.nf` [pedantic_curry] DSL2 - revision: 5c42b1bfea - -WARN: The following invalid input values have been detected: - -* --segmentation_sheet: /mnt/jfs/nextflow/scscape/assets/segmentation.csv -* --features_2_scale: VF -* --scale_method: SCT -* --makeLoupe: true -* --make-loupe: true -* --eula_agreement: Agree -* --test_rds: null -* --test_val: null -* --test_pdf: null -* --validationSchemaIgnoreParams: genomes,igenomes_base -* --validation-schema-ignore-params: genomes,igenomes_base - - - - ------------------------------------------------------- - ,--./,-. - ___ __ __ __ ___ /,-._.--~' - |\ | |__ __ / ` / \ |__) |__ } { - | \| | \__, \__/ | \ |___ \`-._,-`-, - `._,._,' - nf-core/scscape v1.0dev ------------------------------------------------------- -Input/output options - outdir : ../results - -Institutional config options - config_profile_name : Test profile - config_profile_description: Minimal test dataset to check pipeline function - -Max job request options - max_cpus : 4 - max_memory : 10.GB - max_time : 6.h - -Other parameters - sample_sheet : /mnt/jfs/nextflow/scscape/assets/samplesheet.csv - gene_identifier : gene_name - min_cells : 3 - min_features : 200 - nfeature_lower : 10 - nfeature_upper : 0 - ncount_lower : 10 - ncount_upper : 0 - max_mito_pct : 10 - vars_2_regress : nCount_RNA,nFeature_RNA,percent.mt,S.Score,G2M.Score - integration_method : Harmony - resolutions : 0.05,0.1,0.3,0.5,0.7,0.9,1.2,1.5 - -Core Nextflow options - runName : pedantic_curry - containerEngine : docker - launchDir : /mnt/jfs/nextflow/scscape - workDir : /mnt/jfs/nextflow/work - projectDir : /mnt/jfs/nextflow/scscape - userName : rgrindle - profile : test,docker - configFiles : - -!! Only displaying parameters that differ from the pipeline defaults !! ------------------------------------------------------- -If you use nf-core/scscape for your analysis please cite: - -* The nf-core framework - https://doi.org/10.1038/s41587-020-0439-x - -* Software dependencies - https://github.com/nf-core/scscape/blob/master/CITATIONS.md - -WARN: Access to undefined parameter `genomes` -- Initialise it to a default value eg. `params.genomes = some_value` -[- ] NFCORE_SCSCAPE:SCSCAPE:GZIP - - -[- ] NFCORE_SCSCAPE:SCSCAPE:GZIP - -[- ] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - -[- ] NFCORE_SCSCAPE:SCSCAPE:NORMALIZE_QC - - -[- ] NFCORE_SCSCAPE:SCSCAPE:GZIP - -[- ] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - -[- ] NFCORE_SCSCAPE:SCSCAPE:NORMALIZE_QC - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_DOUBLETS - -[- ] NFCORE_SCSCAPE:SCSCAPE:MERGE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:SCALE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_MULT - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_SING - - -[- ] NFCORE_SCSCAPE:SCSCAPE:GZIP - -[- ] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - -[- ] NFCORE_SCSCAPE:SCSCAPE:NORMALIZE_QC - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_DOUBLETS - -[- ] NFCORE_SCSCAPE:SCSCAPE:MERGE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:SCALE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_MULT - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_SING - -[- ] NFCORE_SCSCAPE:SCSCAPE:INTEGRATION - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_NN_CLUSTER - -[- ] NFCORE_SCSCAPE:SCSCAPE:DISPLAY_REDUCTION - - -[- ] NFCORE_SCSCAPE:SCSCAPE:GZIP | 0 of 2 -[- ] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - -[- ] NFCORE_SCSCAPE:SCSCAPE:NORMALIZE_QC - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_DOUBLETS - -[- ] NFCORE_SCSCAPE:SCSCAPE:MERGE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:SCALE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_MULT - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_SING - -[- ] NFCORE_SCSCAPE:SCSCAPE:INTEGRATION - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_NN_CLUSTER - -[- ] NFCORE_SCSCAPE:SCSCAPE:DISPLAY_REDUCTION - -[NFCORE_SCSCAPE:SCSCAPE:GZIP (4)] cache hash: 61b3aa197f0af7f8e8af7e77d0ad0160; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - 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b75b4ff00b9960a0251913f35c3056f5 [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:GZIP - 19c29824aff28c2813b55a60581328f0 [java.lang.String] """ - for file in ${sample_files}/*; do - if [[ \$file != *".gz"* ]]; then - gzip \$file - fi - done - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - GZIP: \$(echo \$(gzip --version| head -n 1| sed 's/gzip //') ) - END_VERSIONS - """ - - f8ad0579d99e80300a9999cf0a963c62 [java.lang.String] quay.io/biocontainers/gzip:1.11 - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - 7779db06e06c396f8ffcf9cd77d1b648 [java.util.LinkedHashMap] [id:2dpa] - 114ffbda19b79872ea642781c51ab77f [java.lang.String] sample_files - e40221bde766fd09997c061fe0d62630 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/assets/test_data/2dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/2dpa, stageName:2dpa)] - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - -[NFCORE_SCSCAPE:SCSCAPE:GZIP (2)] cache hash: 6b49b546f731eb79666b828a89adc563; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - b75b4ff00b9960a0251913f35c3056f5 [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:GZIP - 19c29824aff28c2813b55a60581328f0 [java.lang.String] """ - for file in ${sample_files}/*; do - if [[ \$file != *".gz"* ]]; then - gzip \$file - fi - done - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - GZIP: \$(echo \$(gzip --version| head -n 1| sed 's/gzip //') ) - END_VERSIONS - """ - - f8ad0579d99e80300a9999cf0a963c62 [java.lang.String] quay.io/biocontainers/gzip:1.11 - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - 33894684feb1503fd4d3f17473d9d405 [java.util.LinkedHashMap] [id:1dpa] - 114ffbda19b79872ea642781c51ab77f [java.lang.String] sample_files - f26cbcfe8ef18ecb3398eaab4eafe564 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/assets/test_data/1dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/1dpa, stageName:1dpa)] - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - -[NFCORE_SCSCAPE:SCSCAPE:GZIP (1)] cache hash: f15aef4aff30bbab8f84612733828ece; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - b75b4ff00b9960a0251913f35c3056f5 [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:GZIP - 19c29824aff28c2813b55a60581328f0 [java.lang.String] """ - for file in ${sample_files}/*; do - if [[ \$file != *".gz"* ]]; then - gzip \$file - fi - done - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - GZIP: \$(echo \$(gzip --version| head -n 1| sed 's/gzip //') ) - END_VERSIONS - """ - - f8ad0579d99e80300a9999cf0a963c62 [java.lang.String] quay.io/biocontainers/gzip:1.11 - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - ea4395fd3359a60f12b03ff22d441175 [java.util.LinkedHashMap] [id:0dpa] - 114ffbda19b79872ea642781c51ab77f [java.lang.String] sample_files - 3bf9f94a4ce35b1e9f38010b968bcbf3 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/assets/test_data/0dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/0dpa, stageName:0dpa)] - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - - -executor > float (2) -[9a/9616ae] NFCORE_SCSCAPE:SCSCAPE:GZIP (4dpa) | 0 of 4 -[- ] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - -[- ] NFCORE_SCSCAPE:SCSCAPE:NORMALIZE_QC - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_DOUBLETS - -[- ] NFCORE_SCSCAPE:SCSCAPE:MERGE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:SCALE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_MULT - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_SING - -[- ] NFCORE_SCSCAPE:SCSCAPE:INTEGRATION - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_NN_CLUSTER - -[- ] NFCORE_SCSCAPE:SCSCAPE:DISPLAY_REDUCTION - -[NFCORE_SCSCAPE:SCSCAPE:GZIP (4)] cache hash: 61b3aa197f0af7f8e8af7e77d0ad0160; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - b75b4ff00b9960a0251913f35c3056f5 [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:GZIP - 19c29824aff28c2813b55a60581328f0 [java.lang.String] """ - for file in ${sample_files}/*; do - if [[ \$file != *".gz"* ]]; then - gzip \$file - fi - done - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - GZIP: \$(echo \$(gzip --version| head -n 1| sed 's/gzip //') ) - END_VERSIONS - """ - - f8ad0579d99e80300a9999cf0a963c62 [java.lang.String] quay.io/biocontainers/gzip:1.11 - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - 322f2678e1347a6c51c8d200e7581815 [java.util.LinkedHashMap] [id:4dpa] - 114ffbda19b79872ea642781c51ab77f [java.lang.String] sample_files - 3cc94e1d9d1801f4b4b95117371c916b [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/assets/test_data/4dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/4dpa, stageName:4dpa)] - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - -[NFCORE_SCSCAPE:SCSCAPE:GZIP (3)] cache hash: e1c1fb634b805ac358b142715b6d1b14; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - b75b4ff00b9960a0251913f35c3056f5 [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:GZIP - 19c29824aff28c2813b55a60581328f0 [java.lang.String] """ - for file in ${sample_files}/*; do - if [[ \$file != *".gz"* ]]; then - gzip \$file - fi - done - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - GZIP: \$(echo \$(gzip --version| head -n 1| sed 's/gzip //') ) - END_VERSIONS - """ - - f8ad0579d99e80300a9999cf0a963c62 [java.lang.String] quay.io/biocontainers/gzip:1.11 - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - 7779db06e06c396f8ffcf9cd77d1b648 [java.util.LinkedHashMap] [id:2dpa] - 114ffbda19b79872ea642781c51ab77f [java.lang.String] sample_files - e40221bde766fd09997c061fe0d62630 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/assets/test_data/2dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/2dpa, stageName:2dpa)] - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - -[NFCORE_SCSCAPE:SCSCAPE:GZIP (2)] cache hash: 6b49b546f731eb79666b828a89adc563; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - b75b4ff00b9960a0251913f35c3056f5 [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:GZIP - 19c29824aff28c2813b55a60581328f0 [java.lang.String] """ - for file in ${sample_files}/*; do - if [[ \$file != *".gz"* ]]; then - gzip \$file - fi - done - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - GZIP: \$(echo \$(gzip --version| head -n 1| sed 's/gzip //') ) - END_VERSIONS - """ - - f8ad0579d99e80300a9999cf0a963c62 [java.lang.String] quay.io/biocontainers/gzip:1.11 - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - 33894684feb1503fd4d3f17473d9d405 [java.util.LinkedHashMap] [id:1dpa] - 114ffbda19b79872ea642781c51ab77f [java.lang.String] sample_files - f26cbcfe8ef18ecb3398eaab4eafe564 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/assets/test_data/1dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/1dpa, stageName:1dpa)] - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - -[NFCORE_SCSCAPE:SCSCAPE:GZIP (1)] cache hash: f15aef4aff30bbab8f84612733828ece; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - b75b4ff00b9960a0251913f35c3056f5 [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:GZIP - 19c29824aff28c2813b55a60581328f0 [java.lang.String] """ - for file in ${sample_files}/*; do - if [[ \$file != *".gz"* ]]; then - gzip \$file - fi - done - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - GZIP: \$(echo \$(gzip --version| head -n 1| sed 's/gzip //') ) - END_VERSIONS - """ - - f8ad0579d99e80300a9999cf0a963c62 [java.lang.String] quay.io/biocontainers/gzip:1.11 - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - ea4395fd3359a60f12b03ff22d441175 [java.util.LinkedHashMap] [id:0dpa] - 114ffbda19b79872ea642781c51ab77f [java.lang.String] sample_files - 3bf9f94a4ce35b1e9f38010b968bcbf3 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/assets/test_data/0dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/0dpa, stageName:0dpa)] - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - - -executor > float (3) -[6d/864488] NFCORE_SCSCAPE:SCSCAPE:GZIP (2dpa) | 0 of 4 -[- ] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - -[- ] NFCORE_SCSCAPE:SCSCAPE:NORMALIZE_QC - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_DOUBLETS - -[- ] NFCORE_SCSCAPE:SCSCAPE:MERGE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:SCALE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_MULT - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_SING - -[- ] NFCORE_SCSCAPE:SCSCAPE:INTEGRATION - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_NN_CLUSTER - -[- ] NFCORE_SCSCAPE:SCSCAPE:DISPLAY_REDUCTION - -[NFCORE_SCSCAPE:SCSCAPE:GZIP (4)] cache hash: 61b3aa197f0af7f8e8af7e77d0ad0160; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - b75b4ff00b9960a0251913f35c3056f5 [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:GZIP - 19c29824aff28c2813b55a60581328f0 [java.lang.String] """ - for file in ${sample_files}/*; do - if [[ \$file != *".gz"* ]]; then - gzip \$file - fi - done - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - GZIP: \$(echo \$(gzip --version| head -n 1| sed 's/gzip //') ) - END_VERSIONS - """ - - f8ad0579d99e80300a9999cf0a963c62 [java.lang.String] quay.io/biocontainers/gzip:1.11 - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - 322f2678e1347a6c51c8d200e7581815 [java.util.LinkedHashMap] [id:4dpa] - 114ffbda19b79872ea642781c51ab77f [java.lang.String] sample_files - 3cc94e1d9d1801f4b4b95117371c916b [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/assets/test_data/4dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/4dpa, stageName:4dpa)] - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - -[NFCORE_SCSCAPE:SCSCAPE:GZIP (3)] cache hash: e1c1fb634b805ac358b142715b6d1b14; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - b75b4ff00b9960a0251913f35c3056f5 [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:GZIP - 19c29824aff28c2813b55a60581328f0 [java.lang.String] """ - for file in ${sample_files}/*; do - if [[ \$file != *".gz"* ]]; then - gzip \$file - fi - done - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - GZIP: \$(echo \$(gzip --version| head -n 1| sed 's/gzip //') ) - END_VERSIONS - """ - - f8ad0579d99e80300a9999cf0a963c62 [java.lang.String] quay.io/biocontainers/gzip:1.11 - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - 7779db06e06c396f8ffcf9cd77d1b648 [java.util.LinkedHashMap] [id:2dpa] - 114ffbda19b79872ea642781c51ab77f [java.lang.String] sample_files - e40221bde766fd09997c061fe0d62630 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/assets/test_data/2dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/2dpa, stageName:2dpa)] - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - -[NFCORE_SCSCAPE:SCSCAPE:GZIP (2)] cache hash: 6b49b546f731eb79666b828a89adc563; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - b75b4ff00b9960a0251913f35c3056f5 [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:GZIP - 19c29824aff28c2813b55a60581328f0 [java.lang.String] """ - for file in ${sample_files}/*; do - if [[ \$file != *".gz"* ]]; then - gzip \$file - fi - done - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - GZIP: \$(echo \$(gzip --version| head -n 1| sed 's/gzip //') ) - END_VERSIONS - """ - - f8ad0579d99e80300a9999cf0a963c62 [java.lang.String] quay.io/biocontainers/gzip:1.11 - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - 33894684feb1503fd4d3f17473d9d405 [java.util.LinkedHashMap] [id:1dpa] - 114ffbda19b79872ea642781c51ab77f [java.lang.String] sample_files - f26cbcfe8ef18ecb3398eaab4eafe564 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/assets/test_data/1dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/1dpa, stageName:1dpa)] - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - -[NFCORE_SCSCAPE:SCSCAPE:GZIP (1)] cache hash: f15aef4aff30bbab8f84612733828ece; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - b75b4ff00b9960a0251913f35c3056f5 [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:GZIP - 19c29824aff28c2813b55a60581328f0 [java.lang.String] """ - for file in ${sample_files}/*; do - if [[ \$file != *".gz"* ]]; then - gzip \$file - fi - done - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - GZIP: \$(echo \$(gzip --version| head -n 1| sed 's/gzip //') ) - END_VERSIONS - """ - - f8ad0579d99e80300a9999cf0a963c62 [java.lang.String] quay.io/biocontainers/gzip:1.11 - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - ea4395fd3359a60f12b03ff22d441175 [java.util.LinkedHashMap] [id:0dpa] - 114ffbda19b79872ea642781c51ab77f [java.lang.String] sample_files - 3bf9f94a4ce35b1e9f38010b968bcbf3 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/assets/test_data/0dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/0dpa, stageName:0dpa)] - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - - -executor > float (4) -[c0/9588aa] NFCORE_SCSCAPE:SCSCAPE:GZIP (1dpa) | 0 of 4 -[- ] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - -[- ] NFCORE_SCSCAPE:SCSCAPE:NORMALIZE_QC - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_DOUBLETS - -[- ] NFCORE_SCSCAPE:SCSCAPE:MERGE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:SCALE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_MULT - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_SING - -[- ] NFCORE_SCSCAPE:SCSCAPE:INTEGRATION - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_NN_CLUSTER - -[- ] NFCORE_SCSCAPE:SCSCAPE:DISPLAY_REDUCTION - -[NFCORE_SCSCAPE:SCSCAPE:GZIP (4)] cache hash: 61b3aa197f0af7f8e8af7e77d0ad0160; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - b75b4ff00b9960a0251913f35c3056f5 [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:GZIP - 19c29824aff28c2813b55a60581328f0 [java.lang.String] """ - for file in ${sample_files}/*; do - if [[ \$file != *".gz"* ]]; then - gzip \$file - fi - done - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - GZIP: \$(echo \$(gzip --version| head -n 1| sed 's/gzip //') ) - END_VERSIONS - """ - - f8ad0579d99e80300a9999cf0a963c62 [java.lang.String] quay.io/biocontainers/gzip:1.11 - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - 322f2678e1347a6c51c8d200e7581815 [java.util.LinkedHashMap] [id:4dpa] - 114ffbda19b79872ea642781c51ab77f [java.lang.String] sample_files - 3cc94e1d9d1801f4b4b95117371c916b [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/assets/test_data/4dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/4dpa, stageName:4dpa)] - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - -[NFCORE_SCSCAPE:SCSCAPE:GZIP (3)] cache hash: e1c1fb634b805ac358b142715b6d1b14; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - b75b4ff00b9960a0251913f35c3056f5 [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:GZIP - 19c29824aff28c2813b55a60581328f0 [java.lang.String] """ - for file in ${sample_files}/*; do - if [[ \$file != *".gz"* ]]; then - gzip \$file - fi - done - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - GZIP: \$(echo \$(gzip --version| head -n 1| sed 's/gzip //') ) - END_VERSIONS - """ - - f8ad0579d99e80300a9999cf0a963c62 [java.lang.String] quay.io/biocontainers/gzip:1.11 - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - 7779db06e06c396f8ffcf9cd77d1b648 [java.util.LinkedHashMap] [id:2dpa] - 114ffbda19b79872ea642781c51ab77f [java.lang.String] sample_files - e40221bde766fd09997c061fe0d62630 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/assets/test_data/2dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/2dpa, stageName:2dpa)] - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - -[NFCORE_SCSCAPE:SCSCAPE:GZIP (2)] cache hash: 6b49b546f731eb79666b828a89adc563; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - b75b4ff00b9960a0251913f35c3056f5 [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:GZIP - 19c29824aff28c2813b55a60581328f0 [java.lang.String] """ - for file in ${sample_files}/*; do - if [[ \$file != *".gz"* ]]; then - gzip \$file - fi - done - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - GZIP: \$(echo \$(gzip --version| head -n 1| sed 's/gzip //') ) - END_VERSIONS - """ - - f8ad0579d99e80300a9999cf0a963c62 [java.lang.String] quay.io/biocontainers/gzip:1.11 - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - 33894684feb1503fd4d3f17473d9d405 [java.util.LinkedHashMap] [id:1dpa] - 114ffbda19b79872ea642781c51ab77f [java.lang.String] sample_files - f26cbcfe8ef18ecb3398eaab4eafe564 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/assets/test_data/1dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/1dpa, stageName:1dpa)] - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - -[NFCORE_SCSCAPE:SCSCAPE:GZIP (1)] cache hash: f15aef4aff30bbab8f84612733828ece; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - b75b4ff00b9960a0251913f35c3056f5 [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:GZIP - 19c29824aff28c2813b55a60581328f0 [java.lang.String] """ - for file in ${sample_files}/*; do - if [[ \$file != *".gz"* ]]; then - gzip \$file - fi - done - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - GZIP: \$(echo \$(gzip --version| head -n 1| sed 's/gzip //') ) - END_VERSIONS - """ - - f8ad0579d99e80300a9999cf0a963c62 [java.lang.String] quay.io/biocontainers/gzip:1.11 - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - ea4395fd3359a60f12b03ff22d441175 [java.util.LinkedHashMap] [id:0dpa] - 114ffbda19b79872ea642781c51ab77f [java.lang.String] sample_files - 3bf9f94a4ce35b1e9f38010b968bcbf3 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/assets/test_data/0dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/0dpa, stageName:0dpa)] - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - - -executor > float (4) -[c0/9588aa] NFCORE_SCSCAPE:SCSCAPE:GZIP (1dpa) | 0 of 4 -[- ] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - -[- ] NFCORE_SCSCAPE:SCSCAPE:NORMALIZE_QC - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_DOUBLETS - -[- ] NFCORE_SCSCAPE:SCSCAPE:MERGE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:SCALE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_MULT - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_SING - -[- ] NFCORE_SCSCAPE:SCSCAPE:INTEGRATION - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_NN_CLUSTER - -[- ] NFCORE_SCSCAPE:SCSCAPE:DISPLAY_REDUCTION - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -executor > float (4) -[c0/9588aa] NFCORE_SCSCAPE:SCSCAPE:GZIP (1dpa) | 1 of 4 -[- ] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - -[- ] NFCORE_SCSCAPE:SCSCAPE:NORMALIZE_QC - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_DOUBLETS - -[- ] NFCORE_SCSCAPE:SCSCAPE:MERGE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:SCALE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_MULT - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_SING - -[- ] NFCORE_SCSCAPE:SCSCAPE:INTEGRATION - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_NN_CLUSTER - -[- ] NFCORE_SCSCAPE:SCSCAPE:DISPLAY_REDUCTION - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -executor > float (4) -[c0/9588aa] NFCORE_SCSCAPE:SCSCAPE:GZIP (1dpa) | 1 of 4 -[- ] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - -[- ] NFCORE_SCSCAPE:SCSCAPE:NORMALIZE_QC - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_DOUBLETS - -[- ] NFCORE_SCSCAPE:SCSCAPE:MERGE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:SCALE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_MULT - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_SING - -[- ] NFCORE_SCSCAPE:SCSCAPE:INTEGRATION - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_NN_CLUSTER - -[- ] NFCORE_SCSCAPE:SCSCAPE:DISPLAY_REDUCTION - - -executor > float (4) -[c0/9588aa] NFCORE_SCSCAPE:SCSCAPE:GZIP (1dpa) | 1 of 4 -[- ] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - -[- ] NFCORE_SCSCAPE:SCSCAPE:NORMALIZE_QC - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_DOUBLETS - -[- ] NFCORE_SCSCAPE:SCSCAPE:MERGE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:SCALE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_MULT - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_SING - -[- ] NFCORE_SCSCAPE:SCSCAPE:INTEGRATION - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_NN_CLUSTER - -[- ] NFCORE_SCSCAPE:SCSCAPE:DISPLAY_REDUCTION - - -executor > float (4) -[c0/9588aa] NFCORE_SCSCAPE:SCSCAPE:GZIP (1dpa) | 1 of 4 -[- ] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - -[- ] NFCORE_SCSCAPE:SCSCAPE:NORMALIZE_QC - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_DOUBLETS - -[- ] NFCORE_SCSCAPE:SCSCAPE:MERGE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:SCALE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_MULT - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_SING - -[- ] NFCORE_SCSCAPE:SCSCAPE:INTEGRATION - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_NN_CLUSTER - -[- ] NFCORE_SCSCAPE:SCSCAPE:DISPLAY_REDUCTION - - -executor > float (4) -[6d/864488] NFCORE_SCSCAPE:SCSCAPE:GZIP (2dpa) | 2 of 4 -[- ] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - -[- ] NFCORE_SCSCAPE:SCSCAPE:NORMALIZE_QC - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_DOUBLETS - -[- ] NFCORE_SCSCAPE:SCSCAPE:MERGE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:SCALE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_MULT - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_SING - -[- ] NFCORE_SCSCAPE:SCSCAPE:INTEGRATION - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_NN_CLUSTER - -[- ] NFCORE_SCSCAPE:SCSCAPE:DISPLAY_REDUCTION - - -executor > float (4) -[9a/9616ae] NFCORE_SCSCAPE:SCSCAPE:GZIP (4dpa) | 3 of 4 -[- ] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - -[- ] NFCORE_SCSCAPE:SCSCAPE:NORMALIZE_QC - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_DOUBLETS - -[- ] NFCORE_SCSCAPE:SCSCAPE:MERGE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:SCALE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_MULT - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_SING - -[- ] NFCORE_SCSCAPE:SCSCAPE:INTEGRATION - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_NN_CLUSTER - -[- ] NFCORE_SCSCAPE:SCSCAPE:DISPLAY_REDUCTION - - -executor > float (4) -[bf/96c4c9] NFCORE_SCSCAPE:SCSCAPE:GZIP (0dpa) | 4 of 4 ✔ -[- ] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT | 0 of 4 -[- ] NFCORE_SCSCAPE:SCSCAPE:NORMALIZE_QC - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_DOUBLETS - -[- ] NFCORE_SCSCAPE:SCSCAPE:MERGE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:SCALE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_MULT - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_SING - -[- ] NFCORE_SCSCAPE:SCSCAPE:INTEGRATION - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_NN_CLUSTER - -[- ] NFCORE_SCSCAPE:SCSCAPE:DISPLAY_REDUCTION - -[NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (2)] cache hash: 50acea1226ac4af5b22b3f503fa29ddc; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - 36ee5921d66799ae03c0cef3609c982d [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - 7f89b3a2005251d71bf1230c35cd8227 [java.lang.String] def args = task.ext.args ?: '' - if (genes_2_rm.getClass().name == "nextflow.util.BlankSeparatedList") { - genes_2_rm = 'NULL' - } - """ - MakeSeurat.R \\ - $data_directory \\ - $gene_identifier \\ - $genes_2_rm \\ - ${meta.id} \\ - $min_cells \\ - $min_features \\ - ${args} 2>&1 | tee > 00_${meta.id}_Execution.log - - perl -i -pe 's/"//g;s/\\[\\d\\d?\\d?\\] //g' 00_${meta.id}_InitialValidation.log - - grep -i -E "R version " 00_${meta.id}_InitialVersions.log | perl -pe 's/ version /: \\"/g;s/ \\(.*/\\"/g' >> 00_${meta.id}_FinalVersions.log - perl -ne 'print if /other attached packages:/ .. /^\$/' 00_${meta.id}_InitialVersions.log | grep -v "other" | perl -pe 's/\\\\[.*]\\s+//g;s/\\s+/\\n/g' | grep -v "^\$" | perl -pe 's/_/: \\"/g;s/\$/\\"/' >> 00_${meta.id}_FinalVersions.log - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - R: \$(echo \$(R --version| head -n 1| grep -Eo "[0-9]+[^ ]*"| head -n 1) ) - END_VERSIONS - """ - - 3e3f06d6f2acf4c6657d9b28d0cff53d [java.lang.String] docker.io/mdiblbiocore/seurat:latest - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - 71f4981837fd8efa83dcd0464460c737 [java.util.LinkedHashMap] [id:4dpa, groups:[all, late]] - 0c49bce397edd9800e5f9e47467e383d [java.lang.String] data_directory - 9a555634e392394ca3c00f3da5139b5f [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/work/9a/9616aed5e9b621488d6b32a09d4785/4dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/4dpa, stageName:4dpa)] - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - 71f4981837fd8efa83dcd0464460c737 [java.util.LinkedHashMap] [id:4dpa, groups:[all, late]] - cd36827ed65c23118df291d1043dbcfc [java.lang.String] genes_2_rm - 6ff21ca5414006556a94b50ac6551d9a [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, storePath:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, stageName:danioRerio.aux.features.csv)] - d74a4bb7da916336c7735a32327c97b8 [java.lang.String] min_cells - 3ba1d27b7fde4848a86e865c6c402dfa [java.lang.Integer] 3 - 0ea30274840923c1074b5a8550700c0d [java.lang.String] min_features - 562ef36b46341f12e2997e8bc61c68bd [java.lang.Integer] 200 - 45ad366aeda66e0cd27918150b095317 [java.lang.String] gene_identifier - 2f502e4f4ff1e7d4074a5e8850c729e7 [java.lang.String] gene_name - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - eab359affdb9334848cc02803d7db724 [java.util.HashMap$EntrySet] [task.ext.args=null] - -[NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (1)] cache hash: 863ba4e02b71e9c3accc944634380292; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - 36ee5921d66799ae03c0cef3609c982d [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - 7f89b3a2005251d71bf1230c35cd8227 [java.lang.String] def args = task.ext.args ?: '' - if (genes_2_rm.getClass().name == "nextflow.util.BlankSeparatedList") { - genes_2_rm = 'NULL' - } - """ - MakeSeurat.R \\ - $data_directory \\ - $gene_identifier \\ - $genes_2_rm \\ - ${meta.id} \\ - $min_cells \\ - $min_features \\ - ${args} 2>&1 | tee > 00_${meta.id}_Execution.log - - perl -i -pe 's/"//g;s/\\[\\d\\d?\\d?\\] //g' 00_${meta.id}_InitialValidation.log - - grep -i -E "R version " 00_${meta.id}_InitialVersions.log | perl -pe 's/ version /: \\"/g;s/ \\(.*/\\"/g' >> 00_${meta.id}_FinalVersions.log - perl -ne 'print if /other attached packages:/ .. /^\$/' 00_${meta.id}_InitialVersions.log | grep -v "other" | perl -pe 's/\\\\[.*]\\s+//g;s/\\s+/\\n/g' | grep -v "^\$" | perl -pe 's/_/: \\"/g;s/\$/\\"/' >> 00_${meta.id}_FinalVersions.log - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - R: \$(echo \$(R --version| head -n 1| grep -Eo "[0-9]+[^ ]*"| head -n 1) ) - END_VERSIONS - """ - - 3e3f06d6f2acf4c6657d9b28d0cff53d [java.lang.String] docker.io/mdiblbiocore/seurat:latest - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - bace0eb5a715892251145d036739d766 [java.util.LinkedHashMap] [id:0dpa, groups:[all, early]] - 0c49bce397edd9800e5f9e47467e383d [java.lang.String] data_directory - 7efaa90fe2a5dc75279c15cfb3ba5914 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/work/bf/96c4c96a1e3bd72780d3ea60b78ec9/0dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/0dpa, stageName:0dpa)] - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - bace0eb5a715892251145d036739d766 [java.util.LinkedHashMap] [id:0dpa, groups:[all, early]] - cd36827ed65c23118df291d1043dbcfc [java.lang.String] genes_2_rm - 6ff21ca5414006556a94b50ac6551d9a [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, storePath:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, stageName:danioRerio.aux.features.csv)] - d74a4bb7da916336c7735a32327c97b8 [java.lang.String] min_cells - 3ba1d27b7fde4848a86e865c6c402dfa [java.lang.Integer] 3 - 0ea30274840923c1074b5a8550700c0d [java.lang.String] min_features - 562ef36b46341f12e2997e8bc61c68bd [java.lang.Integer] 200 - 45ad366aeda66e0cd27918150b095317 [java.lang.String] gene_identifier - 2f502e4f4ff1e7d4074a5e8850c729e7 [java.lang.String] gene_name - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - eab359affdb9334848cc02803d7db724 [java.util.HashMap$EntrySet] [task.ext.args=null] - -[NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (4)] cache hash: 65155a337e87272b2e0f37c41bbc0c10; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - 36ee5921d66799ae03c0cef3609c982d [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - 7f89b3a2005251d71bf1230c35cd8227 [java.lang.String] def args = task.ext.args ?: '' - if (genes_2_rm.getClass().name == "nextflow.util.BlankSeparatedList") { - genes_2_rm = 'NULL' - } - """ - MakeSeurat.R \\ - $data_directory \\ - $gene_identifier \\ - $genes_2_rm \\ - ${meta.id} \\ - $min_cells \\ - $min_features \\ - ${args} 2>&1 | tee > 00_${meta.id}_Execution.log - - perl -i -pe 's/"//g;s/\\[\\d\\d?\\d?\\] //g' 00_${meta.id}_InitialValidation.log - - grep -i -E "R version " 00_${meta.id}_InitialVersions.log | perl -pe 's/ version /: \\"/g;s/ \\(.*/\\"/g' >> 00_${meta.id}_FinalVersions.log - perl -ne 'print if /other attached packages:/ .. /^\$/' 00_${meta.id}_InitialVersions.log | grep -v "other" | perl -pe 's/\\\\[.*]\\s+//g;s/\\s+/\\n/g' | grep -v "^\$" | perl -pe 's/_/: \\"/g;s/\$/\\"/' >> 00_${meta.id}_FinalVersions.log - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - R: \$(echo \$(R --version| head -n 1| grep -Eo "[0-9]+[^ ]*"| head -n 1) ) - END_VERSIONS - """ - - 3e3f06d6f2acf4c6657d9b28d0cff53d [java.lang.String] docker.io/mdiblbiocore/seurat:latest - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - 4f45038680ed4bf9a92beeaa81a08136 [java.util.LinkedHashMap] [id:1dpa, groups:[all, early]] - 0c49bce397edd9800e5f9e47467e383d [java.lang.String] data_directory - 46c25cfe6a770ca9f9ad9ffa4066e013 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/work/c0/9588aa0fc4644cd792beba890b5357/1dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/1dpa, stageName:1dpa)] - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - 4f45038680ed4bf9a92beeaa81a08136 [java.util.LinkedHashMap] [id:1dpa, groups:[all, early]] - cd36827ed65c23118df291d1043dbcfc [java.lang.String] genes_2_rm - 6ff21ca5414006556a94b50ac6551d9a [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, storePath:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, stageName:danioRerio.aux.features.csv)] - d74a4bb7da916336c7735a32327c97b8 [java.lang.String] min_cells - 3ba1d27b7fde4848a86e865c6c402dfa [java.lang.Integer] 3 - 0ea30274840923c1074b5a8550700c0d [java.lang.String] min_features - 562ef36b46341f12e2997e8bc61c68bd [java.lang.Integer] 200 - 45ad366aeda66e0cd27918150b095317 [java.lang.String] gene_identifier - 2f502e4f4ff1e7d4074a5e8850c729e7 [java.lang.String] gene_name - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - eab359affdb9334848cc02803d7db724 [java.util.HashMap$EntrySet] [task.ext.args=null] - -[NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (3)] cache hash: 2a2c6a640c371992ac175ae9dbfd6123; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - 36ee5921d66799ae03c0cef3609c982d [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - 7f89b3a2005251d71bf1230c35cd8227 [java.lang.String] def args = task.ext.args ?: '' - if (genes_2_rm.getClass().name == "nextflow.util.BlankSeparatedList") { - genes_2_rm = 'NULL' - } - """ - MakeSeurat.R \\ - $data_directory \\ - $gene_identifier \\ - $genes_2_rm \\ - ${meta.id} \\ - $min_cells \\ - $min_features \\ - ${args} 2>&1 | tee > 00_${meta.id}_Execution.log - - perl -i -pe 's/"//g;s/\\[\\d\\d?\\d?\\] //g' 00_${meta.id}_InitialValidation.log - - grep -i -E "R version " 00_${meta.id}_InitialVersions.log | perl -pe 's/ version /: \\"/g;s/ \\(.*/\\"/g' >> 00_${meta.id}_FinalVersions.log - perl -ne 'print if /other attached packages:/ .. /^\$/' 00_${meta.id}_InitialVersions.log | grep -v "other" | perl -pe 's/\\\\[.*]\\s+//g;s/\\s+/\\n/g' | grep -v "^\$" | perl -pe 's/_/: \\"/g;s/\$/\\"/' >> 00_${meta.id}_FinalVersions.log - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - R: \$(echo \$(R --version| head -n 1| grep -Eo "[0-9]+[^ ]*"| head -n 1) ) - END_VERSIONS - """ - - 3e3f06d6f2acf4c6657d9b28d0cff53d [java.lang.String] docker.io/mdiblbiocore/seurat:latest - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - cc851761240fa0a4f54e36856f3180f7 [java.util.LinkedHashMap] [id:2dpa, groups:[all, late]] - 0c49bce397edd9800e5f9e47467e383d [java.lang.String] data_directory - 0891aea829b581abf57b74dbea6a4798 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/work/6d/8644883f4fc3e198a41c2237019cee/2dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/2dpa, stageName:2dpa)] - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - cc851761240fa0a4f54e36856f3180f7 [java.util.LinkedHashMap] [id:2dpa, groups:[all, late]] - cd36827ed65c23118df291d1043dbcfc [java.lang.String] genes_2_rm - 6ff21ca5414006556a94b50ac6551d9a [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, storePath:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, stageName:danioRerio.aux.features.csv)] - d74a4bb7da916336c7735a32327c97b8 [java.lang.String] min_cells - 3ba1d27b7fde4848a86e865c6c402dfa [java.lang.Integer] 3 - 0ea30274840923c1074b5a8550700c0d [java.lang.String] min_features - 562ef36b46341f12e2997e8bc61c68bd [java.lang.Integer] 200 - 45ad366aeda66e0cd27918150b095317 [java.lang.String] gene_identifier - 2f502e4f4ff1e7d4074a5e8850c729e7 [java.lang.String] gene_name - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - eab359affdb9334848cc02803d7db724 [java.util.HashMap$EntrySet] [task.ext.args=null] - - -executor > float (5) -[bf/96c4c9] NFCORE_SCSCAPE:SCSCAPE:GZIP (0dpa) | 4 of 4 ✔ -[1a/53fa87] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (0dpa) | 0 of 4 -[- ] NFCORE_SCSCAPE:SCSCAPE:NORMALIZE_QC - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_DOUBLETS - -[- ] NFCORE_SCSCAPE:SCSCAPE:MERGE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:SCALE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_MULT - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_SING - -[- ] NFCORE_SCSCAPE:SCSCAPE:INTEGRATION - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_NN_CLUSTER - -[- ] NFCORE_SCSCAPE:SCSCAPE:DISPLAY_REDUCTION - -[NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (2)] cache hash: 50acea1226ac4af5b22b3f503fa29ddc; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - 36ee5921d66799ae03c0cef3609c982d [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - 7f89b3a2005251d71bf1230c35cd8227 [java.lang.String] def args = task.ext.args ?: '' - if (genes_2_rm.getClass().name == "nextflow.util.BlankSeparatedList") { - genes_2_rm = 'NULL' - } - """ - MakeSeurat.R \\ - $data_directory \\ - $gene_identifier \\ - $genes_2_rm \\ - ${meta.id} \\ - $min_cells \\ - $min_features \\ - ${args} 2>&1 | tee > 00_${meta.id}_Execution.log - - perl -i -pe 's/"//g;s/\\[\\d\\d?\\d?\\] //g' 00_${meta.id}_InitialValidation.log - - grep -i -E "R version " 00_${meta.id}_InitialVersions.log | perl -pe 's/ version /: \\"/g;s/ \\(.*/\\"/g' >> 00_${meta.id}_FinalVersions.log - perl -ne 'print if /other attached packages:/ .. /^\$/' 00_${meta.id}_InitialVersions.log | grep -v "other" | perl -pe 's/\\\\[.*]\\s+//g;s/\\s+/\\n/g' | grep -v "^\$" | perl -pe 's/_/: \\"/g;s/\$/\\"/' >> 00_${meta.id}_FinalVersions.log - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - R: \$(echo \$(R --version| head -n 1| grep -Eo "[0-9]+[^ ]*"| head -n 1) ) - END_VERSIONS - """ - - 3e3f06d6f2acf4c6657d9b28d0cff53d [java.lang.String] docker.io/mdiblbiocore/seurat:latest - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - 71f4981837fd8efa83dcd0464460c737 [java.util.LinkedHashMap] [id:4dpa, groups:[all, late]] - 0c49bce397edd9800e5f9e47467e383d [java.lang.String] data_directory - 9a555634e392394ca3c00f3da5139b5f [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/work/9a/9616aed5e9b621488d6b32a09d4785/4dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/4dpa, stageName:4dpa)] - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - 71f4981837fd8efa83dcd0464460c737 [java.util.LinkedHashMap] [id:4dpa, groups:[all, late]] - cd36827ed65c23118df291d1043dbcfc [java.lang.String] genes_2_rm - 6ff21ca5414006556a94b50ac6551d9a [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, storePath:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, stageName:danioRerio.aux.features.csv)] - d74a4bb7da916336c7735a32327c97b8 [java.lang.String] min_cells - 3ba1d27b7fde4848a86e865c6c402dfa [java.lang.Integer] 3 - 0ea30274840923c1074b5a8550700c0d [java.lang.String] min_features - 562ef36b46341f12e2997e8bc61c68bd [java.lang.Integer] 200 - 45ad366aeda66e0cd27918150b095317 [java.lang.String] gene_identifier - 2f502e4f4ff1e7d4074a5e8850c729e7 [java.lang.String] gene_name - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - eab359affdb9334848cc02803d7db724 [java.util.HashMap$EntrySet] [task.ext.args=null] - -[NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (1)] cache hash: 863ba4e02b71e9c3accc944634380292; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - 36ee5921d66799ae03c0cef3609c982d [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - 7f89b3a2005251d71bf1230c35cd8227 [java.lang.String] def args = task.ext.args ?: '' - if (genes_2_rm.getClass().name == "nextflow.util.BlankSeparatedList") { - genes_2_rm = 'NULL' - } - """ - MakeSeurat.R \\ - $data_directory \\ - $gene_identifier \\ - $genes_2_rm \\ - ${meta.id} \\ - $min_cells \\ - $min_features \\ - ${args} 2>&1 | tee > 00_${meta.id}_Execution.log - - perl -i -pe 's/"//g;s/\\[\\d\\d?\\d?\\] //g' 00_${meta.id}_InitialValidation.log - - grep -i -E "R version " 00_${meta.id}_InitialVersions.log | perl -pe 's/ version /: \\"/g;s/ \\(.*/\\"/g' >> 00_${meta.id}_FinalVersions.log - perl -ne 'print if /other attached packages:/ .. /^\$/' 00_${meta.id}_InitialVersions.log | grep -v "other" | perl -pe 's/\\\\[.*]\\s+//g;s/\\s+/\\n/g' | grep -v "^\$" | perl -pe 's/_/: \\"/g;s/\$/\\"/' >> 00_${meta.id}_FinalVersions.log - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - R: \$(echo \$(R --version| head -n 1| grep -Eo "[0-9]+[^ ]*"| head -n 1) ) - END_VERSIONS - """ - - 3e3f06d6f2acf4c6657d9b28d0cff53d [java.lang.String] docker.io/mdiblbiocore/seurat:latest - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - bace0eb5a715892251145d036739d766 [java.util.LinkedHashMap] [id:0dpa, groups:[all, early]] - 0c49bce397edd9800e5f9e47467e383d [java.lang.String] data_directory - 7efaa90fe2a5dc75279c15cfb3ba5914 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/work/bf/96c4c96a1e3bd72780d3ea60b78ec9/0dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/0dpa, stageName:0dpa)] - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - bace0eb5a715892251145d036739d766 [java.util.LinkedHashMap] [id:0dpa, groups:[all, early]] - cd36827ed65c23118df291d1043dbcfc [java.lang.String] genes_2_rm - 6ff21ca5414006556a94b50ac6551d9a [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, storePath:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, stageName:danioRerio.aux.features.csv)] - d74a4bb7da916336c7735a32327c97b8 [java.lang.String] min_cells - 3ba1d27b7fde4848a86e865c6c402dfa [java.lang.Integer] 3 - 0ea30274840923c1074b5a8550700c0d [java.lang.String] min_features - 562ef36b46341f12e2997e8bc61c68bd [java.lang.Integer] 200 - 45ad366aeda66e0cd27918150b095317 [java.lang.String] gene_identifier - 2f502e4f4ff1e7d4074a5e8850c729e7 [java.lang.String] gene_name - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - eab359affdb9334848cc02803d7db724 [java.util.HashMap$EntrySet] [task.ext.args=null] - -[NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (4)] cache hash: 65155a337e87272b2e0f37c41bbc0c10; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - 36ee5921d66799ae03c0cef3609c982d [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - 7f89b3a2005251d71bf1230c35cd8227 [java.lang.String] def args = task.ext.args ?: '' - if (genes_2_rm.getClass().name == "nextflow.util.BlankSeparatedList") { - genes_2_rm = 'NULL' - } - """ - MakeSeurat.R \\ - $data_directory \\ - $gene_identifier \\ - $genes_2_rm \\ - ${meta.id} \\ - $min_cells \\ - $min_features \\ - ${args} 2>&1 | tee > 00_${meta.id}_Execution.log - - perl -i -pe 's/"//g;s/\\[\\d\\d?\\d?\\] //g' 00_${meta.id}_InitialValidation.log - - grep -i -E "R version " 00_${meta.id}_InitialVersions.log | perl -pe 's/ version /: \\"/g;s/ \\(.*/\\"/g' >> 00_${meta.id}_FinalVersions.log - perl -ne 'print if /other attached packages:/ .. /^\$/' 00_${meta.id}_InitialVersions.log | grep -v "other" | perl -pe 's/\\\\[.*]\\s+//g;s/\\s+/\\n/g' | grep -v "^\$" | perl -pe 's/_/: \\"/g;s/\$/\\"/' >> 00_${meta.id}_FinalVersions.log - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - R: \$(echo \$(R --version| head -n 1| grep -Eo "[0-9]+[^ ]*"| head -n 1) ) - END_VERSIONS - """ - - 3e3f06d6f2acf4c6657d9b28d0cff53d [java.lang.String] docker.io/mdiblbiocore/seurat:latest - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - 4f45038680ed4bf9a92beeaa81a08136 [java.util.LinkedHashMap] [id:1dpa, groups:[all, early]] - 0c49bce397edd9800e5f9e47467e383d [java.lang.String] data_directory - 46c25cfe6a770ca9f9ad9ffa4066e013 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/work/c0/9588aa0fc4644cd792beba890b5357/1dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/1dpa, stageName:1dpa)] - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - 4f45038680ed4bf9a92beeaa81a08136 [java.util.LinkedHashMap] [id:1dpa, groups:[all, early]] - cd36827ed65c23118df291d1043dbcfc [java.lang.String] genes_2_rm - 6ff21ca5414006556a94b50ac6551d9a [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, storePath:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, stageName:danioRerio.aux.features.csv)] - d74a4bb7da916336c7735a32327c97b8 [java.lang.String] min_cells - 3ba1d27b7fde4848a86e865c6c402dfa [java.lang.Integer] 3 - 0ea30274840923c1074b5a8550700c0d [java.lang.String] min_features - 562ef36b46341f12e2997e8bc61c68bd [java.lang.Integer] 200 - 45ad366aeda66e0cd27918150b095317 [java.lang.String] gene_identifier - 2f502e4f4ff1e7d4074a5e8850c729e7 [java.lang.String] gene_name - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - eab359affdb9334848cc02803d7db724 [java.util.HashMap$EntrySet] [task.ext.args=null] - -[NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (3)] cache hash: 2a2c6a640c371992ac175ae9dbfd6123; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - 36ee5921d66799ae03c0cef3609c982d [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - 7f89b3a2005251d71bf1230c35cd8227 [java.lang.String] def args = task.ext.args ?: '' - if (genes_2_rm.getClass().name == "nextflow.util.BlankSeparatedList") { - genes_2_rm = 'NULL' - } - """ - MakeSeurat.R \\ - $data_directory \\ - $gene_identifier \\ - $genes_2_rm \\ - ${meta.id} \\ - $min_cells \\ - $min_features \\ - ${args} 2>&1 | tee > 00_${meta.id}_Execution.log - - perl -i -pe 's/"//g;s/\\[\\d\\d?\\d?\\] //g' 00_${meta.id}_InitialValidation.log - - grep -i -E "R version " 00_${meta.id}_InitialVersions.log | perl -pe 's/ version /: \\"/g;s/ \\(.*/\\"/g' >> 00_${meta.id}_FinalVersions.log - perl -ne 'print if /other attached packages:/ .. /^\$/' 00_${meta.id}_InitialVersions.log | grep -v "other" | perl -pe 's/\\\\[.*]\\s+//g;s/\\s+/\\n/g' | grep -v "^\$" | perl -pe 's/_/: \\"/g;s/\$/\\"/' >> 00_${meta.id}_FinalVersions.log - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - R: \$(echo \$(R --version| head -n 1| grep -Eo "[0-9]+[^ ]*"| head -n 1) ) - END_VERSIONS - """ - - 3e3f06d6f2acf4c6657d9b28d0cff53d [java.lang.String] docker.io/mdiblbiocore/seurat:latest - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - cc851761240fa0a4f54e36856f3180f7 [java.util.LinkedHashMap] [id:2dpa, groups:[all, late]] - 0c49bce397edd9800e5f9e47467e383d [java.lang.String] data_directory - 0891aea829b581abf57b74dbea6a4798 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/work/6d/8644883f4fc3e198a41c2237019cee/2dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/2dpa, stageName:2dpa)] - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - cc851761240fa0a4f54e36856f3180f7 [java.util.LinkedHashMap] [id:2dpa, groups:[all, late]] - cd36827ed65c23118df291d1043dbcfc [java.lang.String] genes_2_rm - 6ff21ca5414006556a94b50ac6551d9a [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, storePath:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, stageName:danioRerio.aux.features.csv)] - d74a4bb7da916336c7735a32327c97b8 [java.lang.String] min_cells - 3ba1d27b7fde4848a86e865c6c402dfa [java.lang.Integer] 3 - 0ea30274840923c1074b5a8550700c0d [java.lang.String] min_features - 562ef36b46341f12e2997e8bc61c68bd [java.lang.Integer] 200 - 45ad366aeda66e0cd27918150b095317 [java.lang.String] gene_identifier - 2f502e4f4ff1e7d4074a5e8850c729e7 [java.lang.String] gene_name - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - eab359affdb9334848cc02803d7db724 [java.util.HashMap$EntrySet] [task.ext.args=null] - - -executor > float (6) -[bf/96c4c9] NFCORE_SCSCAPE:SCSCAPE:GZIP (0dpa) | 4 of 4 ✔ -[51/cb1835] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (1dpa) | 0 of 4 -[- ] NFCORE_SCSCAPE:SCSCAPE:NORMALIZE_QC - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_DOUBLETS - -[- ] NFCORE_SCSCAPE:SCSCAPE:MERGE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:SCALE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_MULT - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_SING - -[- ] NFCORE_SCSCAPE:SCSCAPE:INTEGRATION - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_NN_CLUSTER - -[- ] NFCORE_SCSCAPE:SCSCAPE:DISPLAY_REDUCTION - -[NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (2)] cache hash: 50acea1226ac4af5b22b3f503fa29ddc; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - 36ee5921d66799ae03c0cef3609c982d [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - 7f89b3a2005251d71bf1230c35cd8227 [java.lang.String] def args = task.ext.args ?: '' - if (genes_2_rm.getClass().name == "nextflow.util.BlankSeparatedList") { - genes_2_rm = 'NULL' - } - """ - MakeSeurat.R \\ - $data_directory \\ - $gene_identifier \\ - $genes_2_rm \\ - ${meta.id} \\ - $min_cells \\ - $min_features \\ - ${args} 2>&1 | tee > 00_${meta.id}_Execution.log - - perl -i -pe 's/"//g;s/\\[\\d\\d?\\d?\\] //g' 00_${meta.id}_InitialValidation.log - - grep -i -E "R version " 00_${meta.id}_InitialVersions.log | perl -pe 's/ version /: \\"/g;s/ \\(.*/\\"/g' >> 00_${meta.id}_FinalVersions.log - perl -ne 'print if /other attached packages:/ .. /^\$/' 00_${meta.id}_InitialVersions.log | grep -v "other" | perl -pe 's/\\\\[.*]\\s+//g;s/\\s+/\\n/g' | grep -v "^\$" | perl -pe 's/_/: \\"/g;s/\$/\\"/' >> 00_${meta.id}_FinalVersions.log - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - R: \$(echo \$(R --version| head -n 1| grep -Eo "[0-9]+[^ ]*"| head -n 1) ) - END_VERSIONS - """ - - 3e3f06d6f2acf4c6657d9b28d0cff53d [java.lang.String] docker.io/mdiblbiocore/seurat:latest - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - 71f4981837fd8efa83dcd0464460c737 [java.util.LinkedHashMap] [id:4dpa, groups:[all, late]] - 0c49bce397edd9800e5f9e47467e383d [java.lang.String] data_directory - 9a555634e392394ca3c00f3da5139b5f [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/work/9a/9616aed5e9b621488d6b32a09d4785/4dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/4dpa, stageName:4dpa)] - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - 71f4981837fd8efa83dcd0464460c737 [java.util.LinkedHashMap] [id:4dpa, groups:[all, late]] - cd36827ed65c23118df291d1043dbcfc [java.lang.String] genes_2_rm - 6ff21ca5414006556a94b50ac6551d9a [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, storePath:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, stageName:danioRerio.aux.features.csv)] - d74a4bb7da916336c7735a32327c97b8 [java.lang.String] min_cells - 3ba1d27b7fde4848a86e865c6c402dfa [java.lang.Integer] 3 - 0ea30274840923c1074b5a8550700c0d [java.lang.String] min_features - 562ef36b46341f12e2997e8bc61c68bd [java.lang.Integer] 200 - 45ad366aeda66e0cd27918150b095317 [java.lang.String] gene_identifier - 2f502e4f4ff1e7d4074a5e8850c729e7 [java.lang.String] gene_name - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - eab359affdb9334848cc02803d7db724 [java.util.HashMap$EntrySet] [task.ext.args=null] - -[NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (1)] cache hash: 863ba4e02b71e9c3accc944634380292; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - 36ee5921d66799ae03c0cef3609c982d [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - 7f89b3a2005251d71bf1230c35cd8227 [java.lang.String] def args = task.ext.args ?: '' - if (genes_2_rm.getClass().name == "nextflow.util.BlankSeparatedList") { - genes_2_rm = 'NULL' - } - """ - MakeSeurat.R \\ - $data_directory \\ - $gene_identifier \\ - $genes_2_rm \\ - ${meta.id} \\ - $min_cells \\ - $min_features \\ - ${args} 2>&1 | tee > 00_${meta.id}_Execution.log - - perl -i -pe 's/"//g;s/\\[\\d\\d?\\d?\\] //g' 00_${meta.id}_InitialValidation.log - - grep -i -E "R version " 00_${meta.id}_InitialVersions.log | perl -pe 's/ version /: \\"/g;s/ \\(.*/\\"/g' >> 00_${meta.id}_FinalVersions.log - perl -ne 'print if /other attached packages:/ .. /^\$/' 00_${meta.id}_InitialVersions.log | grep -v "other" | perl -pe 's/\\\\[.*]\\s+//g;s/\\s+/\\n/g' | grep -v "^\$" | perl -pe 's/_/: \\"/g;s/\$/\\"/' >> 00_${meta.id}_FinalVersions.log - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - R: \$(echo \$(R --version| head -n 1| grep -Eo "[0-9]+[^ ]*"| head -n 1) ) - END_VERSIONS - """ - - 3e3f06d6f2acf4c6657d9b28d0cff53d [java.lang.String] docker.io/mdiblbiocore/seurat:latest - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - bace0eb5a715892251145d036739d766 [java.util.LinkedHashMap] [id:0dpa, groups:[all, early]] - 0c49bce397edd9800e5f9e47467e383d [java.lang.String] data_directory - 7efaa90fe2a5dc75279c15cfb3ba5914 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/work/bf/96c4c96a1e3bd72780d3ea60b78ec9/0dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/0dpa, stageName:0dpa)] - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - bace0eb5a715892251145d036739d766 [java.util.LinkedHashMap] [id:0dpa, groups:[all, early]] - cd36827ed65c23118df291d1043dbcfc [java.lang.String] genes_2_rm - 6ff21ca5414006556a94b50ac6551d9a [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, storePath:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, stageName:danioRerio.aux.features.csv)] - d74a4bb7da916336c7735a32327c97b8 [java.lang.String] min_cells - 3ba1d27b7fde4848a86e865c6c402dfa [java.lang.Integer] 3 - 0ea30274840923c1074b5a8550700c0d [java.lang.String] min_features - 562ef36b46341f12e2997e8bc61c68bd [java.lang.Integer] 200 - 45ad366aeda66e0cd27918150b095317 [java.lang.String] gene_identifier - 2f502e4f4ff1e7d4074a5e8850c729e7 [java.lang.String] gene_name - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - eab359affdb9334848cc02803d7db724 [java.util.HashMap$EntrySet] [task.ext.args=null] - -[NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (4)] cache hash: 65155a337e87272b2e0f37c41bbc0c10; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - 36ee5921d66799ae03c0cef3609c982d [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - 7f89b3a2005251d71bf1230c35cd8227 [java.lang.String] def args = task.ext.args ?: '' - if (genes_2_rm.getClass().name == "nextflow.util.BlankSeparatedList") { - genes_2_rm = 'NULL' - } - """ - MakeSeurat.R \\ - $data_directory \\ - $gene_identifier \\ - $genes_2_rm \\ - ${meta.id} \\ - $min_cells \\ - $min_features \\ - ${args} 2>&1 | tee > 00_${meta.id}_Execution.log - - perl -i -pe 's/"//g;s/\\[\\d\\d?\\d?\\] //g' 00_${meta.id}_InitialValidation.log - - grep -i -E "R version " 00_${meta.id}_InitialVersions.log | perl -pe 's/ version /: \\"/g;s/ \\(.*/\\"/g' >> 00_${meta.id}_FinalVersions.log - perl -ne 'print if /other attached packages:/ .. /^\$/' 00_${meta.id}_InitialVersions.log | grep -v "other" | perl -pe 's/\\\\[.*]\\s+//g;s/\\s+/\\n/g' | grep -v "^\$" | perl -pe 's/_/: \\"/g;s/\$/\\"/' >> 00_${meta.id}_FinalVersions.log - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - R: \$(echo \$(R --version| head -n 1| grep -Eo "[0-9]+[^ ]*"| head -n 1) ) - END_VERSIONS - """ - - 3e3f06d6f2acf4c6657d9b28d0cff53d [java.lang.String] docker.io/mdiblbiocore/seurat:latest - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - 4f45038680ed4bf9a92beeaa81a08136 [java.util.LinkedHashMap] [id:1dpa, groups:[all, early]] - 0c49bce397edd9800e5f9e47467e383d [java.lang.String] data_directory - 46c25cfe6a770ca9f9ad9ffa4066e013 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/work/c0/9588aa0fc4644cd792beba890b5357/1dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/1dpa, stageName:1dpa)] - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - 4f45038680ed4bf9a92beeaa81a08136 [java.util.LinkedHashMap] [id:1dpa, groups:[all, early]] - cd36827ed65c23118df291d1043dbcfc [java.lang.String] genes_2_rm - 6ff21ca5414006556a94b50ac6551d9a [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, storePath:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, stageName:danioRerio.aux.features.csv)] - d74a4bb7da916336c7735a32327c97b8 [java.lang.String] min_cells - 3ba1d27b7fde4848a86e865c6c402dfa [java.lang.Integer] 3 - 0ea30274840923c1074b5a8550700c0d [java.lang.String] min_features - 562ef36b46341f12e2997e8bc61c68bd [java.lang.Integer] 200 - 45ad366aeda66e0cd27918150b095317 [java.lang.String] gene_identifier - 2f502e4f4ff1e7d4074a5e8850c729e7 [java.lang.String] gene_name - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - eab359affdb9334848cc02803d7db724 [java.util.HashMap$EntrySet] [task.ext.args=null] - -[NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (3)] cache hash: 2a2c6a640c371992ac175ae9dbfd6123; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - 36ee5921d66799ae03c0cef3609c982d [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - 7f89b3a2005251d71bf1230c35cd8227 [java.lang.String] def args = task.ext.args ?: '' - if (genes_2_rm.getClass().name == "nextflow.util.BlankSeparatedList") { - genes_2_rm = 'NULL' - } - """ - MakeSeurat.R \\ - $data_directory \\ - $gene_identifier \\ - $genes_2_rm \\ - ${meta.id} \\ - $min_cells \\ - $min_features \\ - ${args} 2>&1 | tee > 00_${meta.id}_Execution.log - - perl -i -pe 's/"//g;s/\\[\\d\\d?\\d?\\] //g' 00_${meta.id}_InitialValidation.log - - grep -i -E "R version " 00_${meta.id}_InitialVersions.log | perl -pe 's/ version /: \\"/g;s/ \\(.*/\\"/g' >> 00_${meta.id}_FinalVersions.log - perl -ne 'print if /other attached packages:/ .. /^\$/' 00_${meta.id}_InitialVersions.log | grep -v "other" | perl -pe 's/\\\\[.*]\\s+//g;s/\\s+/\\n/g' | grep -v "^\$" | perl -pe 's/_/: \\"/g;s/\$/\\"/' >> 00_${meta.id}_FinalVersions.log - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - R: \$(echo \$(R --version| head -n 1| grep -Eo "[0-9]+[^ ]*"| head -n 1) ) - END_VERSIONS - """ - - 3e3f06d6f2acf4c6657d9b28d0cff53d [java.lang.String] docker.io/mdiblbiocore/seurat:latest - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - cc851761240fa0a4f54e36856f3180f7 [java.util.LinkedHashMap] [id:2dpa, groups:[all, late]] - 0c49bce397edd9800e5f9e47467e383d [java.lang.String] data_directory - 0891aea829b581abf57b74dbea6a4798 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/work/6d/8644883f4fc3e198a41c2237019cee/2dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/2dpa, stageName:2dpa)] - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - cc851761240fa0a4f54e36856f3180f7 [java.util.LinkedHashMap] [id:2dpa, groups:[all, late]] - cd36827ed65c23118df291d1043dbcfc [java.lang.String] genes_2_rm - 6ff21ca5414006556a94b50ac6551d9a [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, storePath:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, stageName:danioRerio.aux.features.csv)] - d74a4bb7da916336c7735a32327c97b8 [java.lang.String] min_cells - 3ba1d27b7fde4848a86e865c6c402dfa [java.lang.Integer] 3 - 0ea30274840923c1074b5a8550700c0d [java.lang.String] min_features - 562ef36b46341f12e2997e8bc61c68bd [java.lang.Integer] 200 - 45ad366aeda66e0cd27918150b095317 [java.lang.String] gene_identifier - 2f502e4f4ff1e7d4074a5e8850c729e7 [java.lang.String] gene_name - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - eab359affdb9334848cc02803d7db724 [java.util.HashMap$EntrySet] [task.ext.args=null] - - -executor > float (7) -[bf/96c4c9] NFCORE_SCSCAPE:SCSCAPE:GZIP (0dpa) | 4 of 4 ✔ -[18/ebde0f] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (4dpa) | 0 of 4 -[- ] NFCORE_SCSCAPE:SCSCAPE:NORMALIZE_QC - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_DOUBLETS - -[- ] NFCORE_SCSCAPE:SCSCAPE:MERGE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:SCALE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_MULT - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_SING - -[- ] NFCORE_SCSCAPE:SCSCAPE:INTEGRATION - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_NN_CLUSTER - -[- ] NFCORE_SCSCAPE:SCSCAPE:DISPLAY_REDUCTION - -[NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (2)] cache hash: 50acea1226ac4af5b22b3f503fa29ddc; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - 36ee5921d66799ae03c0cef3609c982d [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - 7f89b3a2005251d71bf1230c35cd8227 [java.lang.String] def args = task.ext.args ?: '' - if (genes_2_rm.getClass().name == "nextflow.util.BlankSeparatedList") { - genes_2_rm = 'NULL' - } - """ - MakeSeurat.R \\ - $data_directory \\ - $gene_identifier \\ - $genes_2_rm \\ - ${meta.id} \\ - $min_cells \\ - $min_features \\ - ${args} 2>&1 | tee > 00_${meta.id}_Execution.log - - perl -i -pe 's/"//g;s/\\[\\d\\d?\\d?\\] //g' 00_${meta.id}_InitialValidation.log - - grep -i -E "R version " 00_${meta.id}_InitialVersions.log | perl -pe 's/ version /: \\"/g;s/ \\(.*/\\"/g' >> 00_${meta.id}_FinalVersions.log - perl -ne 'print if /other attached packages:/ .. /^\$/' 00_${meta.id}_InitialVersions.log | grep -v "other" | perl -pe 's/\\\\[.*]\\s+//g;s/\\s+/\\n/g' | grep -v "^\$" | perl -pe 's/_/: \\"/g;s/\$/\\"/' >> 00_${meta.id}_FinalVersions.log - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - R: \$(echo \$(R --version| head -n 1| grep -Eo "[0-9]+[^ ]*"| head -n 1) ) - END_VERSIONS - """ - - 3e3f06d6f2acf4c6657d9b28d0cff53d [java.lang.String] docker.io/mdiblbiocore/seurat:latest - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - 71f4981837fd8efa83dcd0464460c737 [java.util.LinkedHashMap] [id:4dpa, groups:[all, late]] - 0c49bce397edd9800e5f9e47467e383d [java.lang.String] data_directory - 9a555634e392394ca3c00f3da5139b5f [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/work/9a/9616aed5e9b621488d6b32a09d4785/4dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/4dpa, stageName:4dpa)] - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - 71f4981837fd8efa83dcd0464460c737 [java.util.LinkedHashMap] [id:4dpa, groups:[all, late]] - cd36827ed65c23118df291d1043dbcfc [java.lang.String] genes_2_rm - 6ff21ca5414006556a94b50ac6551d9a [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, storePath:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, stageName:danioRerio.aux.features.csv)] - d74a4bb7da916336c7735a32327c97b8 [java.lang.String] min_cells - 3ba1d27b7fde4848a86e865c6c402dfa [java.lang.Integer] 3 - 0ea30274840923c1074b5a8550700c0d [java.lang.String] min_features - 562ef36b46341f12e2997e8bc61c68bd [java.lang.Integer] 200 - 45ad366aeda66e0cd27918150b095317 [java.lang.String] gene_identifier - 2f502e4f4ff1e7d4074a5e8850c729e7 [java.lang.String] gene_name - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - eab359affdb9334848cc02803d7db724 [java.util.HashMap$EntrySet] [task.ext.args=null] - -[NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (1)] cache hash: 863ba4e02b71e9c3accc944634380292; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - 36ee5921d66799ae03c0cef3609c982d [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - 7f89b3a2005251d71bf1230c35cd8227 [java.lang.String] def args = task.ext.args ?: '' - if (genes_2_rm.getClass().name == "nextflow.util.BlankSeparatedList") { - genes_2_rm = 'NULL' - } - """ - MakeSeurat.R \\ - $data_directory \\ - $gene_identifier \\ - $genes_2_rm \\ - ${meta.id} \\ - $min_cells \\ - $min_features \\ - ${args} 2>&1 | tee > 00_${meta.id}_Execution.log - - perl -i -pe 's/"//g;s/\\[\\d\\d?\\d?\\] //g' 00_${meta.id}_InitialValidation.log - - grep -i -E "R version " 00_${meta.id}_InitialVersions.log | perl -pe 's/ version /: \\"/g;s/ \\(.*/\\"/g' >> 00_${meta.id}_FinalVersions.log - perl -ne 'print if /other attached packages:/ .. /^\$/' 00_${meta.id}_InitialVersions.log | grep -v "other" | perl -pe 's/\\\\[.*]\\s+//g;s/\\s+/\\n/g' | grep -v "^\$" | perl -pe 's/_/: \\"/g;s/\$/\\"/' >> 00_${meta.id}_FinalVersions.log - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - R: \$(echo \$(R --version| head -n 1| grep -Eo "[0-9]+[^ ]*"| head -n 1) ) - END_VERSIONS - """ - - 3e3f06d6f2acf4c6657d9b28d0cff53d [java.lang.String] docker.io/mdiblbiocore/seurat:latest - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - bace0eb5a715892251145d036739d766 [java.util.LinkedHashMap] [id:0dpa, groups:[all, early]] - 0c49bce397edd9800e5f9e47467e383d [java.lang.String] data_directory - 7efaa90fe2a5dc75279c15cfb3ba5914 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/work/bf/96c4c96a1e3bd72780d3ea60b78ec9/0dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/0dpa, stageName:0dpa)] - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - bace0eb5a715892251145d036739d766 [java.util.LinkedHashMap] [id:0dpa, groups:[all, early]] - cd36827ed65c23118df291d1043dbcfc [java.lang.String] genes_2_rm - 6ff21ca5414006556a94b50ac6551d9a [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, storePath:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, stageName:danioRerio.aux.features.csv)] - d74a4bb7da916336c7735a32327c97b8 [java.lang.String] min_cells - 3ba1d27b7fde4848a86e865c6c402dfa [java.lang.Integer] 3 - 0ea30274840923c1074b5a8550700c0d [java.lang.String] min_features - 562ef36b46341f12e2997e8bc61c68bd [java.lang.Integer] 200 - 45ad366aeda66e0cd27918150b095317 [java.lang.String] gene_identifier - 2f502e4f4ff1e7d4074a5e8850c729e7 [java.lang.String] gene_name - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - eab359affdb9334848cc02803d7db724 [java.util.HashMap$EntrySet] [task.ext.args=null] - -[NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (4)] cache hash: 65155a337e87272b2e0f37c41bbc0c10; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - 36ee5921d66799ae03c0cef3609c982d [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - 7f89b3a2005251d71bf1230c35cd8227 [java.lang.String] def args = task.ext.args ?: '' - if (genes_2_rm.getClass().name == "nextflow.util.BlankSeparatedList") { - genes_2_rm = 'NULL' - } - """ - MakeSeurat.R \\ - $data_directory \\ - $gene_identifier \\ - $genes_2_rm \\ - ${meta.id} \\ - $min_cells \\ - $min_features \\ - ${args} 2>&1 | tee > 00_${meta.id}_Execution.log - - perl -i -pe 's/"//g;s/\\[\\d\\d?\\d?\\] //g' 00_${meta.id}_InitialValidation.log - - grep -i -E "R version " 00_${meta.id}_InitialVersions.log | perl -pe 's/ version /: \\"/g;s/ \\(.*/\\"/g' >> 00_${meta.id}_FinalVersions.log - perl -ne 'print if /other attached packages:/ .. /^\$/' 00_${meta.id}_InitialVersions.log | grep -v "other" | perl -pe 's/\\\\[.*]\\s+//g;s/\\s+/\\n/g' | grep -v "^\$" | perl -pe 's/_/: \\"/g;s/\$/\\"/' >> 00_${meta.id}_FinalVersions.log - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - R: \$(echo \$(R --version| head -n 1| grep -Eo "[0-9]+[^ ]*"| head -n 1) ) - END_VERSIONS - """ - - 3e3f06d6f2acf4c6657d9b28d0cff53d [java.lang.String] docker.io/mdiblbiocore/seurat:latest - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - 4f45038680ed4bf9a92beeaa81a08136 [java.util.LinkedHashMap] [id:1dpa, groups:[all, early]] - 0c49bce397edd9800e5f9e47467e383d [java.lang.String] data_directory - 46c25cfe6a770ca9f9ad9ffa4066e013 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/work/c0/9588aa0fc4644cd792beba890b5357/1dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/1dpa, stageName:1dpa)] - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - 4f45038680ed4bf9a92beeaa81a08136 [java.util.LinkedHashMap] [id:1dpa, groups:[all, early]] - cd36827ed65c23118df291d1043dbcfc [java.lang.String] genes_2_rm - 6ff21ca5414006556a94b50ac6551d9a [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, storePath:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, stageName:danioRerio.aux.features.csv)] - d74a4bb7da916336c7735a32327c97b8 [java.lang.String] min_cells - 3ba1d27b7fde4848a86e865c6c402dfa [java.lang.Integer] 3 - 0ea30274840923c1074b5a8550700c0d [java.lang.String] min_features - 562ef36b46341f12e2997e8bc61c68bd [java.lang.Integer] 200 - 45ad366aeda66e0cd27918150b095317 [java.lang.String] gene_identifier - 2f502e4f4ff1e7d4074a5e8850c729e7 [java.lang.String] gene_name - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - eab359affdb9334848cc02803d7db724 [java.util.HashMap$EntrySet] [task.ext.args=null] - -[NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (3)] cache hash: 2a2c6a640c371992ac175ae9dbfd6123; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - 36ee5921d66799ae03c0cef3609c982d [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - 7f89b3a2005251d71bf1230c35cd8227 [java.lang.String] def args = task.ext.args ?: '' - if (genes_2_rm.getClass().name == "nextflow.util.BlankSeparatedList") { - genes_2_rm = 'NULL' - } - """ - MakeSeurat.R \\ - $data_directory \\ - $gene_identifier \\ - $genes_2_rm \\ - ${meta.id} \\ - $min_cells \\ - $min_features \\ - ${args} 2>&1 | tee > 00_${meta.id}_Execution.log - - perl -i -pe 's/"//g;s/\\[\\d\\d?\\d?\\] //g' 00_${meta.id}_InitialValidation.log - - grep -i -E "R version " 00_${meta.id}_InitialVersions.log | perl -pe 's/ version /: \\"/g;s/ \\(.*/\\"/g' >> 00_${meta.id}_FinalVersions.log - perl -ne 'print if /other attached packages:/ .. /^\$/' 00_${meta.id}_InitialVersions.log | grep -v "other" | perl -pe 's/\\\\[.*]\\s+//g;s/\\s+/\\n/g' | grep -v "^\$" | perl -pe 's/_/: \\"/g;s/\$/\\"/' >> 00_${meta.id}_FinalVersions.log - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - R: \$(echo \$(R --version| head -n 1| grep -Eo "[0-9]+[^ ]*"| head -n 1) ) - END_VERSIONS - """ - - 3e3f06d6f2acf4c6657d9b28d0cff53d [java.lang.String] docker.io/mdiblbiocore/seurat:latest - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - cc851761240fa0a4f54e36856f3180f7 [java.util.LinkedHashMap] [id:2dpa, groups:[all, late]] - 0c49bce397edd9800e5f9e47467e383d [java.lang.String] data_directory - 0891aea829b581abf57b74dbea6a4798 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/work/6d/8644883f4fc3e198a41c2237019cee/2dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/2dpa, stageName:2dpa)] - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - cc851761240fa0a4f54e36856f3180f7 [java.util.LinkedHashMap] [id:2dpa, groups:[all, late]] - cd36827ed65c23118df291d1043dbcfc [java.lang.String] genes_2_rm - 6ff21ca5414006556a94b50ac6551d9a [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, storePath:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, stageName:danioRerio.aux.features.csv)] - d74a4bb7da916336c7735a32327c97b8 [java.lang.String] min_cells - 3ba1d27b7fde4848a86e865c6c402dfa [java.lang.Integer] 3 - 0ea30274840923c1074b5a8550700c0d [java.lang.String] min_features - 562ef36b46341f12e2997e8bc61c68bd [java.lang.Integer] 200 - 45ad366aeda66e0cd27918150b095317 [java.lang.String] gene_identifier - 2f502e4f4ff1e7d4074a5e8850c729e7 [java.lang.String] gene_name - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - eab359affdb9334848cc02803d7db724 [java.util.HashMap$EntrySet] [task.ext.args=null] - - -executor > float (8) -[bf/96c4c9] NFCORE_SCSCAPE:SCSCAPE:GZIP (0dpa) | 4 of 4 ✔ -[ee/bbd3ee] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (2dpa) | 0 of 4 -[- ] NFCORE_SCSCAPE:SCSCAPE:NORMALIZE_QC - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_DOUBLETS - -[- ] NFCORE_SCSCAPE:SCSCAPE:MERGE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:SCALE_SO - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_MULT - -[- ] NFCORE_SCSCAPE:SCSCAPE:PCA_SING - -[- ] NFCORE_SCSCAPE:SCSCAPE:INTEGRATION - -[- ] NFCORE_SCSCAPE:SCSCAPE:FIND_NN_CLUSTER - -[- ] NFCORE_SCSCAPE:SCSCAPE:DISPLAY_REDUCTION - -[NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (2)] cache hash: 50acea1226ac4af5b22b3f503fa29ddc; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - 36ee5921d66799ae03c0cef3609c982d [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - 7f89b3a2005251d71bf1230c35cd8227 [java.lang.String] def args = task.ext.args ?: '' - if (genes_2_rm.getClass().name == "nextflow.util.BlankSeparatedList") { - genes_2_rm = 'NULL' - } - """ - MakeSeurat.R \\ - $data_directory \\ - $gene_identifier \\ - $genes_2_rm \\ - ${meta.id} \\ - $min_cells \\ - $min_features \\ - ${args} 2>&1 | tee > 00_${meta.id}_Execution.log - - perl -i -pe 's/"//g;s/\\[\\d\\d?\\d?\\] //g' 00_${meta.id}_InitialValidation.log - - grep -i -E "R version " 00_${meta.id}_InitialVersions.log | perl -pe 's/ version /: \\"/g;s/ \\(.*/\\"/g' >> 00_${meta.id}_FinalVersions.log - perl -ne 'print if /other attached packages:/ .. /^\$/' 00_${meta.id}_InitialVersions.log | grep -v "other" | perl -pe 's/\\\\[.*]\\s+//g;s/\\s+/\\n/g' | grep -v "^\$" | perl -pe 's/_/: \\"/g;s/\$/\\"/' >> 00_${meta.id}_FinalVersions.log - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - R: \$(echo \$(R --version| head -n 1| grep -Eo "[0-9]+[^ ]*"| head -n 1) ) - END_VERSIONS - """ - - 3e3f06d6f2acf4c6657d9b28d0cff53d [java.lang.String] docker.io/mdiblbiocore/seurat:latest - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - 71f4981837fd8efa83dcd0464460c737 [java.util.LinkedHashMap] [id:4dpa, groups:[all, late]] - 0c49bce397edd9800e5f9e47467e383d [java.lang.String] data_directory - 9a555634e392394ca3c00f3da5139b5f [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/work/9a/9616aed5e9b621488d6b32a09d4785/4dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/4dpa, stageName:4dpa)] - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - 71f4981837fd8efa83dcd0464460c737 [java.util.LinkedHashMap] [id:4dpa, groups:[all, late]] - cd36827ed65c23118df291d1043dbcfc [java.lang.String] genes_2_rm - 6ff21ca5414006556a94b50ac6551d9a [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, storePath:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, stageName:danioRerio.aux.features.csv)] - d74a4bb7da916336c7735a32327c97b8 [java.lang.String] min_cells - 3ba1d27b7fde4848a86e865c6c402dfa [java.lang.Integer] 3 - 0ea30274840923c1074b5a8550700c0d [java.lang.String] min_features - 562ef36b46341f12e2997e8bc61c68bd [java.lang.Integer] 200 - 45ad366aeda66e0cd27918150b095317 [java.lang.String] gene_identifier - 2f502e4f4ff1e7d4074a5e8850c729e7 [java.lang.String] gene_name - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - eab359affdb9334848cc02803d7db724 [java.util.HashMap$EntrySet] [task.ext.args=null] - -[NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (1)] cache hash: 863ba4e02b71e9c3accc944634380292; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - 36ee5921d66799ae03c0cef3609c982d [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - 7f89b3a2005251d71bf1230c35cd8227 [java.lang.String] def args = task.ext.args ?: '' - if (genes_2_rm.getClass().name == "nextflow.util.BlankSeparatedList") { - genes_2_rm = 'NULL' - } - """ - MakeSeurat.R \\ - $data_directory \\ - $gene_identifier \\ - $genes_2_rm \\ - ${meta.id} \\ - $min_cells \\ - $min_features \\ - ${args} 2>&1 | tee > 00_${meta.id}_Execution.log - - perl -i -pe 's/"//g;s/\\[\\d\\d?\\d?\\] //g' 00_${meta.id}_InitialValidation.log - - grep -i -E "R version " 00_${meta.id}_InitialVersions.log | perl -pe 's/ version /: \\"/g;s/ \\(.*/\\"/g' >> 00_${meta.id}_FinalVersions.log - perl -ne 'print if /other attached packages:/ .. /^\$/' 00_${meta.id}_InitialVersions.log | grep -v "other" | perl -pe 's/\\\\[.*]\\s+//g;s/\\s+/\\n/g' | grep -v "^\$" | perl -pe 's/_/: \\"/g;s/\$/\\"/' >> 00_${meta.id}_FinalVersions.log - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - R: \$(echo \$(R --version| head -n 1| grep -Eo "[0-9]+[^ ]*"| head -n 1) ) - END_VERSIONS - """ - - 3e3f06d6f2acf4c6657d9b28d0cff53d [java.lang.String] docker.io/mdiblbiocore/seurat:latest - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - bace0eb5a715892251145d036739d766 [java.util.LinkedHashMap] [id:0dpa, groups:[all, early]] - 0c49bce397edd9800e5f9e47467e383d [java.lang.String] data_directory - 7efaa90fe2a5dc75279c15cfb3ba5914 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/work/bf/96c4c96a1e3bd72780d3ea60b78ec9/0dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/0dpa, stageName:0dpa)] - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - bace0eb5a715892251145d036739d766 [java.util.LinkedHashMap] [id:0dpa, groups:[all, early]] - cd36827ed65c23118df291d1043dbcfc [java.lang.String] genes_2_rm - 6ff21ca5414006556a94b50ac6551d9a [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, storePath:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, stageName:danioRerio.aux.features.csv)] - d74a4bb7da916336c7735a32327c97b8 [java.lang.String] min_cells - 3ba1d27b7fde4848a86e865c6c402dfa [java.lang.Integer] 3 - 0ea30274840923c1074b5a8550700c0d [java.lang.String] min_features - 562ef36b46341f12e2997e8bc61c68bd [java.lang.Integer] 200 - 45ad366aeda66e0cd27918150b095317 [java.lang.String] gene_identifier - 2f502e4f4ff1e7d4074a5e8850c729e7 [java.lang.String] gene_name - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - eab359affdb9334848cc02803d7db724 [java.util.HashMap$EntrySet] [task.ext.args=null] - -[NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (4)] cache hash: 65155a337e87272b2e0f37c41bbc0c10; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - 36ee5921d66799ae03c0cef3609c982d [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - 7f89b3a2005251d71bf1230c35cd8227 [java.lang.String] def args = task.ext.args ?: '' - if (genes_2_rm.getClass().name == "nextflow.util.BlankSeparatedList") { - genes_2_rm = 'NULL' - } - """ - MakeSeurat.R \\ - $data_directory \\ - $gene_identifier \\ - $genes_2_rm \\ - ${meta.id} \\ - $min_cells \\ - $min_features \\ - ${args} 2>&1 | tee > 00_${meta.id}_Execution.log - - perl -i -pe 's/"//g;s/\\[\\d\\d?\\d?\\] //g' 00_${meta.id}_InitialValidation.log - - grep -i -E "R version " 00_${meta.id}_InitialVersions.log | perl -pe 's/ version /: \\"/g;s/ \\(.*/\\"/g' >> 00_${meta.id}_FinalVersions.log - perl -ne 'print if /other attached packages:/ .. /^\$/' 00_${meta.id}_InitialVersions.log | grep -v "other" | perl -pe 's/\\\\[.*]\\s+//g;s/\\s+/\\n/g' | grep -v "^\$" | perl -pe 's/_/: \\"/g;s/\$/\\"/' >> 00_${meta.id}_FinalVersions.log - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - R: \$(echo \$(R --version| head -n 1| grep -Eo "[0-9]+[^ ]*"| head -n 1) ) - END_VERSIONS - """ - - 3e3f06d6f2acf4c6657d9b28d0cff53d [java.lang.String] docker.io/mdiblbiocore/seurat:latest - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - 4f45038680ed4bf9a92beeaa81a08136 [java.util.LinkedHashMap] [id:1dpa, groups:[all, early]] - 0c49bce397edd9800e5f9e47467e383d [java.lang.String] data_directory - 46c25cfe6a770ca9f9ad9ffa4066e013 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/work/c0/9588aa0fc4644cd792beba890b5357/1dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/1dpa, stageName:1dpa)] - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - 4f45038680ed4bf9a92beeaa81a08136 [java.util.LinkedHashMap] [id:1dpa, groups:[all, early]] - cd36827ed65c23118df291d1043dbcfc [java.lang.String] genes_2_rm - 6ff21ca5414006556a94b50ac6551d9a [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, storePath:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, stageName:danioRerio.aux.features.csv)] - d74a4bb7da916336c7735a32327c97b8 [java.lang.String] min_cells - 3ba1d27b7fde4848a86e865c6c402dfa [java.lang.Integer] 3 - 0ea30274840923c1074b5a8550700c0d [java.lang.String] min_features - 562ef36b46341f12e2997e8bc61c68bd [java.lang.Integer] 200 - 45ad366aeda66e0cd27918150b095317 [java.lang.String] gene_identifier - 2f502e4f4ff1e7d4074a5e8850c729e7 [java.lang.String] gene_name - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - eab359affdb9334848cc02803d7db724 [java.util.HashMap$EntrySet] [task.ext.args=null] - -[NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (3)] cache hash: 2a2c6a640c371992ac175ae9dbfd6123; mode: STANDARD; entries: - 9c524029674a0496f357eb24e12d2c5e [java.util.UUID] ddc964c5-be3f-4b82-af89-f0acb4628d31 - 36ee5921d66799ae03c0cef3609c982d [java.lang.String] NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT - 7f89b3a2005251d71bf1230c35cd8227 [java.lang.String] def args = task.ext.args ?: '' - if (genes_2_rm.getClass().name == "nextflow.util.BlankSeparatedList") { - genes_2_rm = 'NULL' - } - """ - MakeSeurat.R \\ - $data_directory \\ - $gene_identifier \\ - $genes_2_rm \\ - ${meta.id} \\ - $min_cells \\ - $min_features \\ - ${args} 2>&1 | tee > 00_${meta.id}_Execution.log - - perl -i -pe 's/"//g;s/\\[\\d\\d?\\d?\\] //g' 00_${meta.id}_InitialValidation.log - - grep -i -E "R version " 00_${meta.id}_InitialVersions.log | perl -pe 's/ version /: \\"/g;s/ \\(.*/\\"/g' >> 00_${meta.id}_FinalVersions.log - perl -ne 'print if /other attached packages:/ .. /^\$/' 00_${meta.id}_InitialVersions.log | grep -v "other" | perl -pe 's/\\\\[.*]\\s+//g;s/\\s+/\\n/g' | grep -v "^\$" | perl -pe 's/_/: \\"/g;s/\$/\\"/' >> 00_${meta.id}_FinalVersions.log - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - R: \$(echo \$(R --version| head -n 1| grep -Eo "[0-9]+[^ ]*"| head -n 1) ) - END_VERSIONS - """ - - 3e3f06d6f2acf4c6657d9b28d0cff53d [java.lang.String] docker.io/mdiblbiocore/seurat:latest - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - cc851761240fa0a4f54e36856f3180f7 [java.util.LinkedHashMap] [id:2dpa, groups:[all, late]] - 0c49bce397edd9800e5f9e47467e383d [java.lang.String] data_directory - 0891aea829b581abf57b74dbea6a4798 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/work/6d/8644883f4fc3e198a41c2237019cee/2dpa, storePath:/mnt/jfs/nextflow/scscape/assets/test_data/2dpa, stageName:2dpa)] - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - cc851761240fa0a4f54e36856f3180f7 [java.util.LinkedHashMap] [id:2dpa, groups:[all, late]] - cd36827ed65c23118df291d1043dbcfc [java.lang.String] genes_2_rm - 6ff21ca5414006556a94b50ac6551d9a [nextflow.util.ArrayBag] [FileHolder(sourceObj:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, storePath:/mnt/jfs/nextflow/scscape/auxillaryGeneFiles/danioRerio.aux.features.csv, stageName:danioRerio.aux.features.csv)] - d74a4bb7da916336c7735a32327c97b8 [java.lang.String] min_cells - 3ba1d27b7fde4848a86e865c6c402dfa [java.lang.Integer] 3 - 0ea30274840923c1074b5a8550700c0d [java.lang.String] min_features - 562ef36b46341f12e2997e8bc61c68bd [java.lang.Integer] 200 - 45ad366aeda66e0cd27918150b095317 [java.lang.String] gene_identifier - 2f502e4f4ff1e7d4074a5e8850c729e7 [java.lang.String] gene_name - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - eab359affdb9334848cc02803d7db724 [java.util.HashMap$EntrySet] [task.ext.args=null] - - -executor > float (8) -[bf/96c4c9] NFC…SCAPE:GZIP (0dpa) | 4 of 4 ✔ -[ee/bbd3ee] NFC…AKE_SEURAT (2dpa) | 0 of 4 -[- ] NFC…CAPE:NORMALIZE_QC - -[- ] NFC…APE:FIND_DOUBLETS - -[- ] NFC…:SCSCAPE:MERGE_SO - -[- ] NFC…:SCSCAPE:SCALE_SO - -[- ] NFC…:SCSCAPE:PCA_MULT - -[- ] NFC…:SCSCAPE:PCA_SING - -[- ] NFC…SCAPE:INTEGRATION - -[- ] NFC…E:FIND_NN_CLUSTER - -[- ] NFC…DISPLAY_REDUCTION - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -executor > float (8) -[bf/96c4c9] NFC…SCAPE:GZIP (0dpa) | 4 of 4 ✔ -[ee/bbd3ee] NFC…AKE_SEURAT (2dpa) | 0 of 4 -[- ] NFC…CAPE:NORMALIZE_QC - -[- ] NFC…APE:FIND_DOUBLETS - -[- ] NFC…:SCSCAPE:MERGE_SO - -[- ] NFC…:SCSCAPE:SCALE_SO - -[- ] NFC…:SCSCAPE:PCA_MULT - -[- ] NFC…:SCSCAPE:PCA_SING - -[- ] NFC…SCAPE:INTEGRATION - -[- ] NFC…E:FIND_NN_CLUSTER - -[- ] NFC…DISPLAY_REDUCTION - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -executor > float (8) -[bf/96c4c9] NFC…SCAPE:GZIP (0dpa) | 4 of 4 ✔ -[ee/bbd3ee] NFC…AKE_SEURAT (2dpa) | 0 of 4 -[- ] NFC…CAPE:NORMALIZE_QC - -[- ] NFC…APE:FIND_DOUBLETS - -[- ] NFC…:SCSCAPE:MERGE_SO - -[- ] NFC…:SCSCAPE:SCALE_SO - -[- ] NFC…:SCSCAPE:PCA_MULT - -[- ] NFC…:SCSCAPE:PCA_SING - -[- ] NFC…SCAPE:INTEGRATION - -[- ] NFC…E:FIND_NN_CLUSTER - -[- ] NFC…DISPLAY_REDUCTION - - -executor > float (8) -[bf/96c4c9] NFC…SCAPE:GZIP (0dpa) | 4 of 4 ✔ -[ee/bbd3ee] NFC…AKE_SEURAT (2dpa) | 0 of 4 -[- ] NFC…CAPE:NORMALIZE_QC - -[- ] NFC…APE:FIND_DOUBLETS - -[- ] NFC…:SCSCAPE:MERGE_SO - -[- ] NFC…:SCSCAPE:SCALE_SO - -[- ] NFC…:SCSCAPE:PCA_MULT - -[- ] NFC…:SCSCAPE:PCA_SING - -[- ] NFC…SCAPE:INTEGRATION - -[- ] NFC…E:FIND_NN_CLUSTER - -[- ] NFC…DISPLAY_REDUCTION - - -executor > float (8) -[bf/96c4c9] NFC…SCAPE:GZIP (0dpa) | 4 of 4 ✔ -[ee/bbd3ee] NFC…AKE_SEURAT (2dpa) | 1 of 5, failed: 1, retries: 1 -[- ] NFC…CAPE:NORMALIZE_QC - -[- ] NFC…APE:FIND_DOUBLETS - -[- ] NFC…:SCSCAPE:MERGE_SO - -[- ] NFC…:SCSCAPE:SCALE_SO - -[- ] NFC…:SCSCAPE:PCA_MULT - -[- ] NFC…:SCSCAPE:PCA_SING - -[- ] NFC…SCAPE:INTEGRATION - -[- ] NFC…E:FIND_NN_CLUSTER - -[- ] NFC…DISPLAY_REDUCTION - -[ee/bbd3ee] NOTE: Process `NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (2dpa)` terminated with an error exit status (1) -- Execution is retried (1) - -executor > float (9) -[bf/96c4c9] NFC…SCAPE:GZIP (0dpa) | 4 of 4 ✔ -[82/06a54c] NFC…AKE_SEURAT (2dpa) | 1 of 5, failed: 1, retries: 1 -[- ] NFC…CAPE:NORMALIZE_QC - -[- ] NFC…APE:FIND_DOUBLETS - -[- ] NFC…:SCSCAPE:MERGE_SO - -[- ] NFC…:SCSCAPE:SCALE_SO - -[- ] NFC…:SCSCAPE:PCA_MULT - -[- ] NFC…:SCSCAPE:PCA_SING - -[- ] NFC…SCAPE:INTEGRATION - -[- ] NFC…E:FIND_NN_CLUSTER - -[- ] NFC…DISPLAY_REDUCTION - -[ee/bbd3ee] NOTE: Process `NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (2dpa)` terminated with an error exit status (1) -- Execution is retried (1) - -executor > float (9) -[bf/96c4c9] NFC…SCAPE:GZIP (0dpa) | 4 of 4 ✔ -[51/cb1835] NFC…AKE_SEURAT (1dpa) | 2 of 6, failed: 2, retries: 2 -[- ] NFC…CAPE:NORMALIZE_QC - -[- ] NFC…APE:FIND_DOUBLETS - -[- ] NFC…:SCSCAPE:MERGE_SO - -[- ] NFC…:SCSCAPE:SCALE_SO - -[- ] NFC…:SCSCAPE:PCA_MULT - -[- ] NFC…:SCSCAPE:PCA_SING - -[- ] NFC…SCAPE:INTEGRATION - -[- ] NFC…E:FIND_NN_CLUSTER - -[- ] NFC…DISPLAY_REDUCTION - -[ee/bbd3ee] NOTE: Process `NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (2dpa)` terminated with an error exit status (1) -- Execution is retried (1) -[51/cb1835] NOTE: Process `NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (1dpa)` terminated with an error exit status (1) -- Execution is retried (1) - -executor > float (10) -[bf/96c4c9] NFC…SCAPE:GZIP (0dpa) | 4 of 4 ✔ -[57/536fc7] NFC…AKE_SEURAT (1dpa) | 2 of 6, failed: 2, retries: 2 -[- ] NFC…CAPE:NORMALIZE_QC - -[- ] NFC…APE:FIND_DOUBLETS - -[- ] NFC…:SCSCAPE:MERGE_SO - -[- ] NFC…:SCSCAPE:SCALE_SO - -[- ] NFC…:SCSCAPE:PCA_MULT - -[- ] NFC…:SCSCAPE:PCA_SING - -[- ] NFC…SCAPE:INTEGRATION - -[- ] NFC…E:FIND_NN_CLUSTER - -[- ] NFC…DISPLAY_REDUCTION - -[ee/bbd3ee] NOTE: Process `NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (2dpa)` terminated with an error exit status (1) -- Execution is retried (1) -[51/cb1835] NOTE: Process `NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (1dpa)` terminated with an error exit status (1) -- Execution is retried (1) - -executor > float (10) -[bf/96c4c9] NFC…SCAPE:GZIP (0dpa) | 4 of 4 ✔ -[1a/53fa87] NFC…AKE_SEURAT (0dpa) | 3 of 7, failed: 3, retries: 3 -[- ] NFC…CAPE:NORMALIZE_QC - -[- ] NFC…APE:FIND_DOUBLETS - -[- ] NFC…:SCSCAPE:MERGE_SO - -[- ] NFC…:SCSCAPE:SCALE_SO - -[- ] NFC…:SCSCAPE:PCA_MULT - -[- ] NFC…:SCSCAPE:PCA_SING - -[- ] NFC…SCAPE:INTEGRATION - -[- ] NFC…E:FIND_NN_CLUSTER - -[- ] NFC…DISPLAY_REDUCTION - -[ee/bbd3ee] NOTE: Process `NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (2dpa)` terminated with an error exit status (1) -- Execution is retried (1) -[51/cb1835] NOTE: Process `NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (1dpa)` terminated with an error exit status (1) -- Execution is retried (1) -[1a/53fa87] NOTE: Process `NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (0dpa)` terminated with an error exit status (1) -- Execution is retried (1) - -executor > float (11) -[bf/96c4c9] NFC…SCAPE:GZIP (0dpa) | 4 of 4 ✔ -[93/672b14] NFC…AKE_SEURAT (0dpa) | 4 of 8, failed: 4, retries: 4 -[- ] NFC…CAPE:NORMALIZE_QC - -[- ] NFC…APE:FIND_DOUBLETS - -[- ] NFC…:SCSCAPE:MERGE_SO - -[- ] NFC…:SCSCAPE:SCALE_SO - -[- ] NFC…:SCSCAPE:PCA_MULT - -[- ] NFC…:SCSCAPE:PCA_SING - -[- ] NFC…SCAPE:INTEGRATION - -[- ] NFC…E:FIND_NN_CLUSTER - -[- ] NFC…DISPLAY_REDUCTION - -[ee/bbd3ee] NOTE: Process `NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (2dpa)` terminated with an error exit status (1) -- Execution is retried (1) -[51/cb1835] NOTE: Process `NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (1dpa)` terminated with an error exit status (1) -- Execution is retried (1) -[1a/53fa87] NOTE: Process `NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (0dpa)` terminated with an error exit status (1) -- Execution is retried (1) -[18/ebde0f] NOTE: Process `NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (4dpa)` terminated with an error exit status (1) -- Execution is retried (1) - -executor > float (12) -[bf/96c4c9] NFC…SCAPE:GZIP (0dpa) | 4 of 4 ✔ -[31/5fe94f] NFC…AKE_SEURAT (4dpa) | 4 of 8, failed: 4, retries: 4 -[- ] NFC…CAPE:NORMALIZE_QC - -[- ] NFC…APE:FIND_DOUBLETS - -[- ] NFC…:SCSCAPE:MERGE_SO - -[- ] NFC…:SCSCAPE:SCALE_SO - -[- ] NFC…:SCSCAPE:PCA_MULT - -[- ] NFC…:SCSCAPE:PCA_SING - -[- ] NFC…SCAPE:INTEGRATION - -[- ] NFC…E:FIND_NN_CLUSTER - -[- ] NFC…DISPLAY_REDUCTION - -[ee/bbd3ee] NOTE: Process `NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (2dpa)` terminated with an error exit status (1) -- Execution is retried (1) -[51/cb1835] NOTE: Process `NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (1dpa)` terminated with an error exit status (1) -- Execution is retried (1) -[1a/53fa87] NOTE: Process `NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (0dpa)` terminated with an error exit status (1) -- Execution is retried (1) -[18/ebde0f] NOTE: Process `NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (4dpa)` terminated with an error exit status (1) -- Execution is retried (1) - -executor > float (12) -[bf/96c4c9] NFC…SCAPE:GZIP (0dpa) | 4 of 4 ✔ -[31/5fe94f] NFC…AKE_SEURAT (4dpa) | 4 of 8, failed: 4, retries: 4 -[- ] NFC…CAPE:NORMALIZE_QC - -[- ] NFC…APE:FIND_DOUBLETS - -[- ] NFC…:SCSCAPE:MERGE_SO - -[- ] NFC…:SCSCAPE:SCALE_SO - -[- ] NFC…:SCSCAPE:PCA_MULT - -[- ] NFC…:SCSCAPE:PCA_SING - -[- ] NFC…SCAPE:INTEGRATION - -[- ] NFC…E:FIND_NN_CLUSTER - -[- ] NFC…DISPLAY_REDUCTION - - - - - - -executor > float (12) -[bf/96c4c9] NFC…SCAPE:GZIP (0dpa) | 4 of 4 ✔ -[31/5fe94f] NFC…AKE_SEURAT (4dpa) | 4 of 8, failed: 4, retries: 4 -[- ] NFC…CAPE:NORMALIZE_QC - -[- ] NFC…APE:FIND_DOUBLETS - -[- ] NFC…:SCSCAPE:MERGE_SO - -[- ] NFC…:SCSCAPE:SCALE_SO - -[- ] NFC…:SCSCAPE:PCA_MULT - -[- ] NFC…:SCSCAPE:PCA_SING - -[- ] NFC…SCAPE:INTEGRATION - -[- ] NFC…E:FIND_NN_CLUSTER - -[- ] NFC…DISPLAY_REDUCTION - - - - - - -executor > float (12) -[bf/96c4c9] NFC…SCAPE:GZIP (0dpa) | 4 of 4 ✔ -[31/5fe94f] NFC…AKE_SEURAT (4dpa) | 4 of 8, failed: 4, retries: 4 -[- ] NFC…CAPE:NORMALIZE_QC - -[- ] NFC…APE:FIND_DOUBLETS - -[- ] NFC…:SCSCAPE:MERGE_SO - -[- ] NFC…:SCSCAPE:SCALE_SO - -[- ] NFC…:SCSCAPE:PCA_MULT - -[- ] NFC…:SCSCAPE:PCA_SING - -[- ] NFC…SCAPE:INTEGRATION - -[- ] NFC…E:FIND_NN_CLUSTER - -[- ] NFC…DISPLAY_REDUCTION - - -executor > float (12) -[bf/96c4c9] NFC…SCAPE:GZIP (0dpa) | 4 of 4 ✔ -[31/5fe94f] NFC…AKE_SEURAT (4dpa) | 4 of 8, failed: 4, retries: 4 -[- ] NFC…CAPE:NORMALIZE_QC - -[- ] NFC…APE:FIND_DOUBLETS - -[- ] NFC…:SCSCAPE:MERGE_SO - -[- ] NFC…:SCSCAPE:SCALE_SO - -[- ] NFC…:SCSCAPE:PCA_MULT - -[- ] NFC…:SCSCAPE:PCA_SING - -[- ] NFC…SCAPE:INTEGRATION - -[- ] NFC…E:FIND_NN_CLUSTER - -[- ] NFC…DISPLAY_REDUCTION - - -executor > float (12) -[bf/96c4c9] NFC…SCAPE:GZIP (0dpa) | 4 of 4 ✔ -[31/5fe94f] NFC…AKE_SEURAT (4dpa) | 4 of 8, failed: 4, retries: 4 -[- ] NFC…CAPE:NORMALIZE_QC - -[- ] NFC…APE:FIND_DOUBLETS - -[- ] NFC…:SCSCAPE:MERGE_SO - -[- ] NFC…:SCSCAPE:SCALE_SO - -[- ] NFC…:SCSCAPE:PCA_MULT - -[- ] NFC…:SCSCAPE:PCA_SING - -[- ] NFC…SCAPE:INTEGRATION - -[- ] NFC…E:FIND_NN_CLUSTER - -[- ] NFC…DISPLAY_REDUCTION - -ERROR ~ Error executing process > 'NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (2dpa)' - -Caused by: - Process `NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (2dpa)` terminated with an error exit status (1) - - -Command executed: - - MakeSeurat.R \ - 2dpa \ - gene_name \ - danioRerio.aux.features.csv \ - 2dpa \ - 3 \ - 200 \ - 2>&1 | tee > 00_2dpa_Execution.log - - perl -i -pe 's/"//g;s/\[\d\d?\d?\] //g' 00_2dpa_InitialValidation.log - - grep -i -E "R version " 00_2dpa_InitialVersions.log | perl -pe 's/ version /: \"/g;s/ \(.*/\"/g' >> 00_2dpa_FinalVersions.log - perl -ne 'print if /other attached packages:/ .. /^$/' 00_2dpa_InitialVersions.log | grep -v "other" | perl -pe 's/\\[.*]\s+//g;s/\s+/\n/g' | grep -v "^$" | perl -pe 's/_/: \"/g;s/$/\"/' >> 00_2dpa_FinalVersions.log - - cat <<-END_VERSIONS > versions.yml - "NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT": - R: $(echo $(R --version| head -n 1| grep -Eo "[0-9]+[^ ]*"| head -n 1) ) - END_VERSIONS - -Command exit status: - 1 - -Command output: - (empty) - -Work dir: - /mnt/jfs/nextflow/work/82/06a54c189644566bbbbfdb7ee48d3a - -Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh` - - -- Check '.nextflow.log' file for details --[nf-core/scscape] Pipeline completed with errors- -WARN: Killing running tasks (3) - -executor > float (12) -[bf/96c4c9] NFC…SCAPE:GZIP (0dpa) | 4 of 4 ✔ -[31/5fe94f] NFC…AKE_SEURAT (4dpa) | 5 of 5, failed: 5, retries: 4 -[- ] NFC…CAPE:NORMALIZE_QC - -[- ] NFC…APE:FIND_DOUBLETS - -[- ] NFC…:SCSCAPE:MERGE_SO - -[- ] NFC…:SCSCAPE:SCALE_SO - -[- ] NFC…:SCSCAPE:PCA_MULT - -[- ] NFC…:SCSCAPE:PCA_SING - -[- ] NFC…SCAPE:INTEGRATION - -[- ] NFC…E:FIND_NN_CLUSTER - -[- ] NFC…DISPLAY_REDUCTION - -ERROR ~ Error executing process > 'NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (2dpa)' - -Caused by: - Process `NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT (2dpa)` terminated with an error exit status (1) - - -Command executed: - - MakeSeurat.R \ - 2dpa \ - gene_name \ - danioRerio.aux.features.csv \ - 2dpa \ - 3 \ - 200 \ - 2>&1 | tee > 00_2dpa_Execution.log - - perl -i -pe 's/"//g;s/\[\d\d?\d?\] //g' 00_2dpa_InitialValidation.log - - grep -i -E "R version " 00_2dpa_InitialVersions.log | perl -pe 's/ version /: \"/g;s/ \(.*/\"/g' >> 00_2dpa_FinalVersions.log - perl -ne 'print if /other attached packages:/ .. /^$/' 00_2dpa_InitialVersions.log | grep -v "other" | perl -pe 's/\\[.*]\s+//g;s/\s+/\n/g' | grep -v "^$" | perl -pe 's/_/: \"/g;s/$/\"/' >> 00_2dpa_FinalVersions.log - - cat <<-END_VERSIONS > versions.yml - "NFCORE_SCSCAPE:SCSCAPE:MAKE_SEURAT": - R: $(echo $(R --version| head -n 1| grep -Eo "[0-9]+[^ ]*"| head -n 1) ) - END_VERSIONS - -Command exit status: - 1 - -Command output: - (empty) - -Work dir: - /mnt/jfs/nextflow/work/82/06a54c189644566bbbbfdb7ee48d3a - -Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh` - - -- Check '.nextflow.log' file for details - diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index 04f5aa8..584770e 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -46,15 +46,5 @@ class WorkflowMain { // Check input has been provided } - // - // Get attribute from genome config file e.g. fasta - // - public static Object getGenomeAttribute(params, attribute) { - if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) { - if (params.genomes[ params.genome ].containsKey(attribute)) { - return params.genomes[ params.genome ][ attribute ] - } - } - return null - } + } diff --git a/nextflow.config b/nextflow.config index 738e96a..2a8e592 100644 --- a/nextflow.config +++ b/nextflow.config @@ -64,6 +64,7 @@ params { hook_url = null help = false version = false + genomes = null // Config options config_profile_name = null