From 117884c783977964fe3ee9196ebbc44944f2eaa3 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 11 Dec 2024 10:39:08 +0100 Subject: [PATCH] add human_gencode_filter to starfusion build --- CHANGELOG.md | 3 +- modules/local/fusioncatcher/download/main.nf | 1 - modules/local/starfusion/build/main.nf | 1 + subworkflows/local/arriba_workflow.nf | 2 +- test.xml | 240 +++++++++++++++++++ 5 files changed, 244 insertions(+), 3 deletions(-) create mode 100644 test.xml diff --git a/CHANGELOG.md b/CHANGELOG.md index 1980cd86..a1444c08 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -27,7 +27,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Updated to nf-core/tools 3.0.2 [#504](https://github.com/nf-core/rnafusion/pull/504) - Remove local module `RRNA_TRANSCRIPTS` (replaced by nf-core module) [#541](https://github.com/nf-core/rnafusion/pull/541) - Allow fastq files without a dot before .fn(.gz)/.fastq(.gz) files [#548](https://github.com/nf-core/rnafusion/pull/548) - ext.args = "-genePredExt -geneNameAsName2 -ignoreGroupsWithoutExons" GTF_TO_REFFLAT + ext.args = "-genePredExt -geneNameAsName2 -ignoreGroupsWithoutExons" GTF_TO_REFFLAT + ### Fixed - Fixed some Nextflow run-commands in the docs [#491](https://github.com/nf-core/rnafusion/pull/491) diff --git a/modules/local/fusioncatcher/download/main.nf b/modules/local/fusioncatcher/download/main.nf index ed97c834..03c0a1f3 100644 --- a/modules/local/fusioncatcher/download/main.nf +++ b/modules/local/fusioncatcher/download/main.nf @@ -19,7 +19,6 @@ process FUSIONCATCHER_DOWNLOAD { script: def args = task.ext.args ?: '' - def args2 = task.ext.args2 ?: '' // TODO: move to S3 // def url = diff --git a/modules/local/starfusion/build/main.nf b/modules/local/starfusion/build/main.nf index 436a5e4f..10485ac0 100644 --- a/modules/local/starfusion/build/main.nf +++ b/modules/local/starfusion/build/main.nf @@ -33,6 +33,7 @@ process STARFUSION_BUILD { --pfam_db Pfam-A.hmm \\ --dfam_db homo_sapiens_dfam.hmm \\ --max_readlength $params.read_length \\ + --human_gencode_filter \\ --CPU $task.cpus cat <<-END_VERSIONS > versions.yml diff --git a/subworkflows/local/arriba_workflow.nf b/subworkflows/local/arriba_workflow.nf index 5d844678..5575f5c0 100644 --- a/subworkflows/local/arriba_workflow.nf +++ b/subworkflows/local/arriba_workflow.nf @@ -52,7 +52,7 @@ workflow ARRIBA_WORKFLOW { } else { ch_arriba_fusions = reads.combine(Channel.value( file(ch_dummy_file, checkIfExists:true ) ) ) - .map { meta, reads, fusions -> [ meta, fusions ] } + .map { it -> [ it[0], it[2] ] } ch_arriba_fusion_fail = ch_dummy_file } diff --git a/test.xml b/test.xml new file mode 100644 index 00000000..2aed29e1 --- /dev/null +++ b/test.xml @@ -0,0 +1,240 @@ +Nextflow stdout: + +N E X T F L O W ~ version 24.10.2 +Launching `/Users/annick.renevey/Projects/rnafusion/tests/../main.nf` [elated_pasteur] DSL2 - revision: dc78081240 + +------------------------------------------------------ + ,--./,-. + ___ __ __ __ ___ /,-._.--~' + |\ | |__ __ / ` / \ |__) |__ } { + | \| | \__, \__/ | \ |___ \`-._,-`-, + `._,._,' + nf-core/rnafusion 4.0.0dev +------------------------------------------------------ +Input/output options + input : https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv + outdir : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/acc69f529568702c4fabd8a30cf1fcb0/output + genomes_base : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/acc69f529568702c4fabd8a30cf1fcb0/output/references + genome_gencode_version : 46 + starfusion_build : true + all : true + arriba_ref_blacklist : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/acc69f529568702c4fabd8a30cf1fcb0/output/references/arriba/blacklist_hg38_GRCh38_v2.4.0.tsv.gz + arriba_ref_cytobands : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/acc69f529568702c4fabd8a30cf1fcb0/output/references/arriba/cytobands_hg38_GRCh38_v2.4.0.tsv + arriba_ref_known_fusions : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/acc69f529568702c4fabd8a30cf1fcb0/output/references/arriba/known_fusions_hg38_GRCh38_v2.4.0.tsv.gz + arriba_ref_protein_domains : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/acc69f529568702c4fabd8a30cf1fcb0/output/references/arriba/protein_domains_hg38_GRCh38_v2.4.0.gff3 + gencode_ref : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/acc69f529568702c4fabd8a30cf1fcb0/output/references/gencode + fusioncatcher_limitSjdbInsertNsj : 2000000 + fusioncatcher_ref : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/acc69f529568702c4fabd8a30cf1fcb0/output/references/fusioncatcher/human_v46 + fusioncatcher_ref_stub_check : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/acc69f529568702c4fabd8a30cf1fcb0/output/references/fusioncatcher/human_v46/ensembl_fully_overlapping_genes.txt + fusioninspector_limitSjdbInsertNsj: 1000000 + fusionreport_ref : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/acc69f529568702c4fabd8a30cf1fcb0/output/references/fusion_report_db + fusionreport_ref_stub_check : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/acc69f529568702c4fabd8a30cf1fcb0/output/references/fusion_report_db/mitelman.db + hgnc_ref : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/acc69f529568702c4fabd8a30cf1fcb0/output/references/hgnc/hgnc_complete_set.txt + hgnc_date : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/acc69f529568702c4fabd8a30cf1fcb0/output/references/hgnc/HGNC-DB-timestamp.txt + salmon_index : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/acc69f529568702c4fabd8a30cf1fcb0/output/references/salmon/salmon + salmon_index_stub_check : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/acc69f529568702c4fabd8a30cf1fcb0/output/references/salmon/salmon/complete_ref_lens.bin + starfusion_ref : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/acc69f529568702c4fabd8a30cf1fcb0/output/references/starfusion/ctat_genome_lib_build_dir + starfusion_ref_stub_check : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/acc69f529568702c4fabd8a30cf1fcb0/output/references/starfusion/Pfam-A.hmm + starindex_ref : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/acc69f529568702c4fabd8a30cf1fcb0/output/references/star + starindex_ref_stub_check : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/acc69f529568702c4fabd8a30cf1fcb0/output/references/star/star/Genome + tools_cutoff : 1 + +Read trimming options + fastp_trim : true + adapter_fasta : [] + +Alignment compression options + cram : [] + +Reference genome options + fasta : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/acc69f529568702c4fabd8a30cf1fcb0/output/references/gencode/Homo_sapiens_GRCh38_46_dna_primary_assembly.fa + fai : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/acc69f529568702c4fabd8a30cf1fcb0/output/references/gencode/Homo_sapiens_GRCh38_46_dna_primary_assembly.fa.fai + genome : GRCh38 + gtf : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/acc69f529568702c4fabd8a30cf1fcb0/output/references/gencode/Homo_sapiens_GRCh38_46.gtf + refflat : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/acc69f529568702c4fabd8a30cf1fcb0/output/references/gencode/Homo_sapiens_GRCh38_46.gtf.refflat + rrna_intervals : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/acc69f529568702c4fabd8a30cf1fcb0/output/references/gencode/Homo_sapiens_GRCh38_46.interval_list + no_cosmic : true + +Institutional config options + config_profile_name : Test profile + config_profile_description : Minimal test dataset to check pipeline function + +Core Nextflow options + runName : elated_pasteur + containerEngine : docker + launchDir : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/acc69f529568702c4fabd8a30cf1fcb0 + workDir : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/acc69f529568702c4fabd8a30cf1fcb0/work + projectDir : /Users/annick.renevey/Projects/rnafusion + userName : annick.renevey + profile : test,docker + configFiles :  + +!! Only displaying parameters that differ from the pipeline defaults !! +------------------------------------------------------ +* The nf-core framework + https://doi.org/10.1038/s41587-020-0439-x + +* Software dependencies + https://github.com/nf-core/rnafusion/blob/master/CITATIONS.md + +WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected. +HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`. + +WARN: Skipping COSMIC DB download from `FUSIONREPORT_DOWNLOAD` and skip using it in `FUSIONREPORT` +[13/a75f51] Submitted process > NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:FUSIONCATCHER_BUILD (fusioncatcher_build) +[78/f27e8a] Submitted process > NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD (hgnc) +[c9/d109b6] Submitted process > NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:ARRIBA_DOWNLOAD (arriba) +[1b/cb8505] Submitted process > NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:GENCODE_DOWNLOAD (gencode_download) +[61/738ba4] Submitted process > NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:FUSIONREPORT_DOWNLOAD (fusionreport) +[6c/ccb83a] Submitted process > NFCORE_RNAFUSION:RNAFUSION:FASTQC (test) +[52/593378] Submitted process > NFCORE_RNAFUSION:RNAFUSION:TRIM_WORKFLOW:FASTP (test) +[18/18b5f3] Submitted process > NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:SAMTOOLS_FAIDX (Homo_sapiens.GRCh38.46_dna_primary_assembly.fa) +[38/36e8dd] Submitted process > NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:GATK4_CREATESEQUENCEDICTIONARY (Homo_sapiens.GRCh38.46_dna_primary_assembly.fa) +[b3/7aad17] Submitted process > NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:GET_RRNA_TRANSCRIPTS (get_rrna_bed) +[53/e4d111] Submitted process > NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:STAR_GENOMEGENERATE (Homo_sapiens.GRCh38.46_dna_primary_assembly.fa) +[37/d0930c] Submitted process > NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:GFFREAD (Homo_sapiens.GRCh38.46.gtf) +[26/aa9b36] Submitted process > NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:GTF_TO_REFFLAT (Homo_sapiens.GRCh38.46.gtf) +[18/66b9c3] Submitted process > NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:STARFUSION_BUILD (star-fusion) +[05/6e1246] Submitted process > NFCORE_RNAFUSION:RNAFUSION:TRIM_WORKFLOW:FASTQC_FOR_FASTP (test) +[83/52bcc1] Submitted process > NFCORE_RNAFUSION:RNAFUSION:FUSIONCATCHER_WORKFLOW:FUSIONCATCHER (test) +[5b/c0d7bc] Submitted process > NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:GATK4_BEDTOINTERVALLIST (Homo_sapiens.GRCh38.46.gtf) +[24/c5d0b9] Submitted process > NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STAR_FOR_STARFUSION (test) +[43/8be8df] Submitted process > NFCORE_RNAFUSION:RNAFUSION:ARRIBA_WORKFLOW:STAR_FOR_ARRIBA (test) +[f9/87735b] Submitted process > NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:SALMON_INDEX (Homo_sapiens.GRCh38.46.gtf.fasta) +[b4/64a1cd] Submitted process > NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:PICARD_COLLECTRNASEQMETRICS (test) +[cc/99a46b] Submitted process > NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:PICARD_COLLECTINSERTSIZEMETRICS (test) +[0b/18a022] Submitted process > NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (test) +[aa/000cc3] Submitted process > NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:SAMTOOLS_INDEX_FOR_STARFUSION (test) +[3d/4dfbba] Submitted process > NFCORE_RNAFUSION:RNAFUSION:STRINGTIE_WORKFLOW:STRINGTIE_STRINGTIE (test) +[10/6bc883] Submitted process > NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:GATK4_MARKDUPLICATES (test) +[74/397e36] Submitted process > NFCORE_RNAFUSION:RNAFUSION:ARRIBA_WORKFLOW:ARRIBA_ARRIBA (test) +[df/483739] Submitted process > NFCORE_RNAFUSION:RNAFUSION:SALMON_QUANT (test) +[92/376a4b] Submitted process > NFCORE_RNAFUSION:RNAFUSION:STRINGTIE_WORKFLOW:STRINGTIE_MERGE (1) +[b6/26ca21] Submitted process > NFCORE_RNAFUSION:RNAFUSION:FUSIONREPORT_WORKFLOW:FUSIONREPORT (test) +[51/2177ee] Submitted process > NFCORE_RNAFUSION:RNAFUSION:MULTIQC +-[nf-core/rnafusion] Pipeline completed successfully- +Nextflow stderr: + +Nextflow stdout: + +N E X T F L O W ~ version 24.10.2 +Launching `/Users/annick.renevey/Projects/rnafusion/tests/../main.nf` [naughty_becquerel] DSL2 - revision: dc78081240 + +------------------------------------------------------ + ,--./,-. + ___ __ __ __ ___ /,-._.--~' + |\ | |__ __ / ` / \ |__) |__ } { + | \| | \__, \__/ | \ |___ \`-._,-`-, + `._,._,' + nf-core/rnafusion 4.0.0dev +------------------------------------------------------ +Input/output options + input : https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv + outdir : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/5d4f02e50caba01d5f317164e187f7c1/output + genomes_base : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/5d4f02e50caba01d5f317164e187f7c1/output/references + genome_gencode_version : 46 + starfusion_build : true + all : true + arriba_ref_blacklist : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/5d4f02e50caba01d5f317164e187f7c1/output/references/arriba/blacklist_hg38_GRCh38_v2.4.0.tsv.gz + arriba_ref_cytobands : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/5d4f02e50caba01d5f317164e187f7c1/output/references/arriba/cytobands_hg38_GRCh38_v2.4.0.tsv + arriba_ref_known_fusions : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/5d4f02e50caba01d5f317164e187f7c1/output/references/arriba/known_fusions_hg38_GRCh38_v2.4.0.tsv.gz + arriba_ref_protein_domains : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/5d4f02e50caba01d5f317164e187f7c1/output/references/arriba/protein_domains_hg38_GRCh38_v2.4.0.gff3 + gencode_ref : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/5d4f02e50caba01d5f317164e187f7c1/output/references/gencode + fusioncatcher_limitSjdbInsertNsj : 2000000 + fusioncatcher_ref : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/5d4f02e50caba01d5f317164e187f7c1/output/references/fusioncatcher/human_v46 + fusioncatcher_ref_stub_check : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/5d4f02e50caba01d5f317164e187f7c1/output/references/fusioncatcher/human_v46/ensembl_fully_overlapping_genes.txt + fusioninspector_limitSjdbInsertNsj: 1000000 + fusionreport_ref : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/5d4f02e50caba01d5f317164e187f7c1/output/references/fusion_report_db + fusionreport_ref_stub_check : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/5d4f02e50caba01d5f317164e187f7c1/output/references/fusion_report_db/mitelman.db + hgnc_ref : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/5d4f02e50caba01d5f317164e187f7c1/output/references/hgnc/hgnc_complete_set.txt + hgnc_date : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/5d4f02e50caba01d5f317164e187f7c1/output/references/hgnc/HGNC-DB-timestamp.txt + salmon_index : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/5d4f02e50caba01d5f317164e187f7c1/output/references/salmon/salmon + salmon_index_stub_check : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/5d4f02e50caba01d5f317164e187f7c1/output/references/salmon/salmon/complete_ref_lens.bin + starfusion_ref : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/5d4f02e50caba01d5f317164e187f7c1/output/references/starfusion/ctat_genome_lib_build_dir + starfusion_ref_stub_check : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/5d4f02e50caba01d5f317164e187f7c1/output/references/starfusion/Pfam-A.hmm + starindex_ref : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/5d4f02e50caba01d5f317164e187f7c1/output/references/star + starindex_ref_stub_check : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/5d4f02e50caba01d5f317164e187f7c1/output/references/star/star/Genome + tools_cutoff : 1 + +Read trimming options + adapter_fasta : [] + +Alignment compression options + cram : [] + +Reference genome options + fasta : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/5d4f02e50caba01d5f317164e187f7c1/output/references/gencode/Homo_sapiens_GRCh38_46_dna_primary_assembly.fa + fai : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/5d4f02e50caba01d5f317164e187f7c1/output/references/gencode/Homo_sapiens_GRCh38_46_dna_primary_assembly.fa.fai + genome : GRCh38 + gtf : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/5d4f02e50caba01d5f317164e187f7c1/output/references/gencode/Homo_sapiens_GRCh38_46.gtf + refflat : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/5d4f02e50caba01d5f317164e187f7c1/output/references/gencode/Homo_sapiens_GRCh38_46.gtf.refflat + rrna_intervals : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/5d4f02e50caba01d5f317164e187f7c1/output/references/gencode/Homo_sapiens_GRCh38_46.interval_list + no_cosmic : true + +Institutional config options + config_profile_name : Test profile + config_profile_description : Minimal test dataset to check pipeline function + +Core Nextflow options + runName : naughty_becquerel + containerEngine : docker + launchDir : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/5d4f02e50caba01d5f317164e187f7c1 + workDir : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/5d4f02e50caba01d5f317164e187f7c1/work + projectDir : /Users/annick.renevey/Projects/rnafusion + userName : annick.renevey + profile : test,docker + configFiles :  + +!! Only displaying parameters that differ from the pipeline defaults !! +------------------------------------------------------ +* The nf-core framework + https://doi.org/10.1038/s41587-020-0439-x + +* Software dependencies + https://github.com/nf-core/rnafusion/blob/master/CITATIONS.md + +WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected. +HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`. + +WARN: Skipping COSMIC DB download from `FUSIONREPORT_DOWNLOAD` and skip using it in `FUSIONREPORT` +[8d/ee20bb] Submitted process > NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD (hgnc) +[d6/69323a] Submitted process > NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:GENCODE_DOWNLOAD (gencode_download) +[b9/5c89ae] Submitted process > NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:FUSIONREPORT_DOWNLOAD (fusionreport) +[43/355279] Submitted process > NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:FUSIONCATCHER_BUILD (fusioncatcher_build) +[94/cf96bf] Submitted process > NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:ARRIBA_DOWNLOAD (arriba) +[e4/d33580] Submitted process > NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:GATK4_CREATESEQUENCEDICTIONARY (Homo_sapiens.GRCh38.46_dna_primary_assembly.fa) +[db/fa3dd4] Submitted process > NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:SAMTOOLS_FAIDX (Homo_sapiens.GRCh38.46_dna_primary_assembly.fa) +[90/118532] Submitted process > NFCORE_RNAFUSION:RNAFUSION:FASTQC (test) +[b9/6593b4] Submitted process > NFCORE_RNAFUSION:RNAFUSION:TRIM_WORKFLOW:FASTP (test) +[b4/28611c] Submitted process > NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:GTF_TO_REFFLAT (Homo_sapiens.GRCh38.46.gtf) +[d0/9b767c] Submitted process > NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:GET_RRNA_TRANSCRIPTS (get_rrna_bed) +[c2/fd36fd] Submitted process > NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:GFFREAD (Homo_sapiens.GRCh38.46.gtf) +[76/b9b243] Submitted process > NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:STAR_GENOMEGENERATE (Homo_sapiens.GRCh38.46_dna_primary_assembly.fa) +[d6/350166] Submitted process > NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:STARFUSION_BUILD (star-fusion) +[89/c38359] Submitted process > NFCORE_RNAFUSION:RNAFUSION:TRIM_WORKFLOW:FASTQC_FOR_FASTP (test) +[92/431af8] Submitted process > NFCORE_RNAFUSION:RNAFUSION:FUSIONCATCHER_WORKFLOW:FUSIONCATCHER (test) +[43/c4079e] Submitted process > NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:GATK4_BEDTOINTERVALLIST (Homo_sapiens.GRCh38.46.gtf) +[e6/3c5e19] Submitted process > NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:SALMON_INDEX (Homo_sapiens.GRCh38.46.gtf.fasta) +[71/f9cbec] Submitted process > NFCORE_RNAFUSION:RNAFUSION:ARRIBA_WORKFLOW:STAR_FOR_ARRIBA (test) +[96/59d525] Submitted process > NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STAR_FOR_STARFUSION (test) +[99/6d4d21] Submitted process > NFCORE_RNAFUSION:RNAFUSION:SALMON_QUANT (test) +[9c/fd7ac5] Submitted process > NFCORE_RNAFUSION:RNAFUSION:ARRIBA_WORKFLOW:ARRIBA_ARRIBA (test) +[29/6b167b] Submitted process > NFCORE_RNAFUSION:RNAFUSION:STRINGTIE_WORKFLOW:STRINGTIE_STRINGTIE (test) +[39/c6c23e] Submitted process > NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (test) +[35/474e2f] Submitted process > NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:SAMTOOLS_INDEX_FOR_STARFUSION (test) +[66/b0ff6a] Submitted process > NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:GATK4_MARKDUPLICATES (test) +[63/a246b6] Submitted process > NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:PICARD_COLLECTRNASEQMETRICS (test) +[41/50018c] Submitted process > NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:PICARD_COLLECTINSERTSIZEMETRICS (test) +[8c/96974e] Submitted process > NFCORE_RNAFUSION:RNAFUSION:STRINGTIE_WORKFLOW:STRINGTIE_MERGE (1) +[fe/e581e9] Submitted process > NFCORE_RNAFUSION:RNAFUSION:FUSIONREPORT_WORKFLOW:FUSIONREPORT (test) +[99/47d296] Submitted process > NFCORE_RNAFUSION:RNAFUSION:MULTIQC +-[nf-core/rnafusion] Pipeline completed successfully- +Nextflow stderr: + + \ No newline at end of file