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test: update stub structure
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@atrigila
atrigila committed Dec 12, 2024
1 parent 99033b5 commit 17dd8b4
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Showing 2 changed files with 167 additions and 36 deletions.
97 changes: 72 additions & 25 deletions modules/local/starfusion/build/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -34,41 +34,88 @@ process STARFUSION_BUILD {

stub:
"""
mkdir ctat_genome_lib_build_dir
mkdir -p ctat_genome_lib_build_dir
touch ctat_genome_lib_build_dir/AnnotFilterRule.pm
gzip -c /dev/null > ctat_genome_lib_build_dir/PFAM.domtblout.dat.gz
touch ctat_genome_lib_build_dir/ref_annot.gtf.gene_spans
touch ctat_genome_lib_build_dir/ref_genome.fa.mm2
touch ctat_genome_lib_build_dir/ref_genome.fa.ntf
gzip -c /dev/null > ctat_genome_lib_build_dir/blast_pairs.dat.gz
touch ctat_genome_lib_build_dir/ref_annot.cdna.fa
touch ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
touch ctat_genome_lib_build_dir/ref_genome.fa.ndb
touch ctat_genome_lib_build_dir/ref_genome.fa.nto
touch ctat_genome_lib_build_dir/blast_pairs.idx
mkdir -p ctat_genome_lib_build_dir/__chkpts
touch ctat_genome_lib_build_dir/__chkpts/annotfiltrule_cp.ok
touch ctat_genome_lib_build_dir/__chkpts/blast_pairs.idx.ok
touch ctat_genome_lib_build_dir/__chkpts/cp_gene_blast_pairs.ok
touch ctat_genome_lib_build_dir/__chkpts/cp_pfam_dat.ok
touch ctat_genome_lib_build_dir/__chkpts/cp_ref_annot_cdna.ok
touch ctat_genome_lib_build_dir/__chkpts/fusion_annot_lib.cp.ok
touch ctat_genome_lib_build_dir/__chkpts/_fusion_annot_lib.idx.ok
touch ctat_genome_lib_build_dir/__chkpts/index_pfam_hits.ok
touch ctat_genome_lib_build_dir/__chkpts/index_ref_annot_cdna.ok
touch ctat_genome_lib_build_dir/__chkpts/makeblastdb.ok
touch ctat_genome_lib_build_dir/__chkpts/mm2_genome_idx.ok
touch ctat_genome_lib_build_dir/__chkpts/mm2.splice_bed.ok
touch ctat_genome_lib_build_dir/__chkpts/_prot_info_db.ok
touch ctat_genome_lib_build_dir/__chkpts/ref_annot.cdsplus.dfam_masked.fa.cp.ok
touch ctat_genome_lib_build_dir/__chkpts/ref_annot.cdsplus.dfam_masked.fa.idx.ok
touch ctat_genome_lib_build_dir/__chkpts/ref_annot.gtf.gene_spans.ok
touch ctat_genome_lib_build_dir/__chkpts/ref_annot.gtf.mini.sortu.ok
touch ctat_genome_lib_build_dir/__chkpts/ref_annot.gtf.ok
touch ctat_genome_lib_build_dir/__chkpts/ref_genome_fai.ok
touch ctat_genome_lib_build_dir/__chkpts/ref_genome.fa.ok
touch ctat_genome_lib_build_dir/__chkpts/trans.blast.dat.cp.ok
touch ctat_genome_lib_build_dir/__chkpts/trans.blast.dat.index.ok
touch ctat_genome_lib_build_dir/__chkpts/validate_ctat_genome_lib.ok
gzip -c /dev/null > ctat_genome_lib_build_dir/fusion_annot_lib.gz
touch ctat_genome_lib_build_dir/fusion_annot_lib.idx
touch ctat_genome_lib_build_dir/pfam_domains.dbm
gzip -c /dev/null > ctat_genome_lib_build_dir/PFAM.domtblout.dat.gz
touch ctat_genome_lib_build_dir/ref_annot.cdna.fa
touch ctat_genome_lib_build_dir/ref_annot.cdna.fa.idx
touch ctat_genome_lib_build_dir/ref_annot.gtf.mm2.splice.bed
touch ctat_genome_lib_build_dir/ref_genome.fa.nhr
touch ctat_genome_lib_build_dir/ref_genome.fa.star.idx
touch ctat_genome_lib_build_dir/__chkpts
touch ctat_genome_lib_build_dir/ref_annot.cds
touch ctat_genome_lib_build_dir/ref_annot.pep
touch ctat_genome_lib_build_dir/ref_genome.fa.nin
touch ctat_genome_lib_build_dir/trans.blast.align_coords.align_coords.dat
gzip -c /dev/null > ctat_genome_lib_build_dir/fusion_annot_lib.gz
touch ctat_genome_lib_build_dir/ref_annot.cdsplus.fa
touch ctat_genome_lib_build_dir/ref_annot.prot_info.dbm
touch ctat_genome_lib_build_dir/ref_genome.fa.njs
touch ctat_genome_lib_build_dir/trans.blast.align_coords.align_coords.dbm
touch ctat_genome_lib_build_dir/fusion_annot_lib.idx
touch ctat_genome_lib_build_dir/ref_annot.cdsplus.fa.idx
touch ctat_genome_lib_build_dir/ref_genome.fa
touch ctat_genome_lib_build_dir/ref_genome.fa.not
gzip -c /dev/null > ctat_genome_lib_build_dir/trans.blast.dat.gz
touch ctat_genome_lib_build_dir/pfam_domains.dbm
touch ctat_genome_lib_build_dir/ref_annot.gtf
touch ctat_genome_lib_build_dir/ref_annot.gtf.gene_spans
touch ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
touch ctat_genome_lib_build_dir/ref_annot.gtf.mm2.splice.bed
touch ctat_genome_lib_build_dir/ref_annot.pep
touch ctat_genome_lib_build_dir/ref_annot.prot_info.dbm
touch ctat_genome_lib_build_dir/ref_genome.fa
touch ctat_genome_lib_build_dir/ref_genome.fa.fai
touch ctat_genome_lib_build_dir/ref_genome.fa.mm2
touch ctat_genome_lib_build_dir/ref_genome.fa.ndb
touch ctat_genome_lib_build_dir/ref_genome.fa.nhr
touch ctat_genome_lib_build_dir/ref_genome.fa.nin
touch ctat_genome_lib_build_dir/ref_genome.fa.njs
touch ctat_genome_lib_build_dir/ref_genome.fa.not
touch ctat_genome_lib_build_dir/ref_genome.fa.nsq
touch ctat_genome_lib_build_dir/ref_genome.fa.ntf
touch ctat_genome_lib_build_dir/ref_genome.fa.nto
mkdir -p ctat_genome_lib_build_dir/ref_genome.fa.star.idx
touch ctat_genome_lib_build_dir/ref_genome.fa.star.idx/build.ok
touch ctat_genome_lib_build_dir/ref_genome.fa.star.idx/chrLength.txt
touch ctat_genome_lib_build_dir/ref_genome.fa.star.idx/chrNameLength.txt
touch ctat_genome_lib_build_dir/ref_genome.fa.star.idx/chrName.txt
touch ctat_genome_lib_build_dir/ref_genome.fa.star.idx/chrStart.txt
touch ctat_genome_lib_build_dir/ref_genome.fa.star.idx/exonGeTrInfo.tab
touch ctat_genome_lib_build_dir/ref_genome.fa.star.idx/exonInfo.tab
touch ctat_genome_lib_build_dir/ref_genome.fa.star.idx/geneInfo.tab
touch ctat_genome_lib_build_dir/ref_genome.fa.star.idx/Genome
touch ctat_genome_lib_build_dir/ref_genome.fa.star.idx/genomeParameters.txt
touch ctat_genome_lib_build_dir/ref_genome.fa.star.idx/Log.out
touch ctat_genome_lib_build_dir/ref_genome.fa.star.idx/SA
touch ctat_genome_lib_build_dir/ref_genome.fa.star.idx/SAindex
touch ctat_genome_lib_build_dir/ref_genome.fa.star.idx/sjdbInfo.txt
touch ctat_genome_lib_build_dir/ref_genome.fa.star.idx/sjdbList.fromGTF.out.tab
touch ctat_genome_lib_build_dir/ref_genome.fa.star.idx/sjdbList.out.tab
touch ctat_genome_lib_build_dir/ref_genome.fa.star.idx/transcriptInfo.tab
touch ctat_genome_lib_build_dir/trans.blast.align_coords.align_coords.dat
touch ctat_genome_lib_build_dir/trans.blast.align_coords.align_coords.dbm
gzip -c /dev/null > ctat_genome_lib_build_dir/trans.blast.dat.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand Down
106 changes: 95 additions & 11 deletions modules/local/starfusion/build/tests/main.nf.test.snap
View file
Original file line number Diff line number Diff line change
Expand Up @@ -62,12 +62,12 @@
"exonGeTrInfo.tab:md5,3c35618d07a8e35a0f9108699fcdda42",
"exonInfo.tab:md5,bcbb3f32fa31fe504cc737f337ad341c",
"geneInfo.tab:md5,db5db4b6e003904e9908fce7c05f0125",
"Genome:md5,9e3efdd0901cabb5a2d589664a63b372",
"Genome:md5,21aac51c5062f73d6305ae77691f5d4e",
true,
true,
"SA:md5,7dd9083264be9c6a2194d990bc10d237",
"SAindex:md5,ac4711df685109e04356db9e9cb9fb7f",
"sjdbInfo.txt:md5,e4cc1bbf8bd687cfc3d7c2c702e6def7",
"SA:md5,4d6ee7c82328aa304300e51ab5677ff9",
"SAindex:md5,2d3498f7d84a69bbc65fe9de1887820c",
"sjdbInfo.txt:md5,0ad0c108e6d02ec541d6adeffbdea6fd",
"sjdbList.fromGTF.out.tab:md5,8f3e8604b00d4067e4eb80aa476a8113",
"sjdbList.out.tab:md5,5d78dd49d5db24ca2c056b7ebe5c2059",
"transcriptInfo.tab:md5,b758c0ccaddcf0453bab5905b3cec4a2",
Expand All @@ -80,7 +80,7 @@
"nf-test": "0.9.0",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-11T15:32:32.307712922"
"timestamp": "2024-12-12T14:57:13.528134845"
},
"STARFUSION_BUILD - human - minigenome - stub": {
"content": [
Expand All @@ -93,7 +93,31 @@
[
"AnnotFilterRule.pm:md5,d41d8cd98f00b204e9800998ecf8427e",
"PFAM.domtblout.dat.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
"__chkpts:md5,d41d8cd98f00b204e9800998ecf8427e",
[
"_fusion_annot_lib.idx.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"_prot_info_db.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"annotfiltrule_cp.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"blast_pairs.idx.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"cp_gene_blast_pairs.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"cp_pfam_dat.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"cp_ref_annot_cdna.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"fusion_annot_lib.cp.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"index_pfam_hits.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"index_ref_annot_cdna.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"makeblastdb.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"mm2.splice_bed.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"mm2_genome_idx.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"ref_annot.cdsplus.dfam_masked.fa.cp.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"ref_annot.cdsplus.dfam_masked.fa.idx.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"ref_annot.gtf.gene_spans.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"ref_annot.gtf.mini.sortu.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"ref_annot.gtf.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"ref_genome.fa.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"ref_genome_fai.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"trans.blast.dat.cp.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"trans.blast.dat.index.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"validate_ctat_genome_lib.ok:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"blast_pairs.dat.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
"blast_pairs.idx:md5,d41d8cd98f00b204e9800998ecf8427e",
"fusion_annot_lib.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
Expand Down Expand Up @@ -121,7 +145,25 @@
"ref_genome.fa.nsq:md5,d41d8cd98f00b204e9800998ecf8427e",
"ref_genome.fa.ntf:md5,d41d8cd98f00b204e9800998ecf8427e",
"ref_genome.fa.nto:md5,d41d8cd98f00b204e9800998ecf8427e",
"ref_genome.fa.star.idx:md5,d41d8cd98f00b204e9800998ecf8427e",
[
"Genome:md5,d41d8cd98f00b204e9800998ecf8427e",
"Log.out:md5,d41d8cd98f00b204e9800998ecf8427e",
"SA:md5,d41d8cd98f00b204e9800998ecf8427e",
"SAindex:md5,d41d8cd98f00b204e9800998ecf8427e",
"build.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"chrLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"chrName.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"chrNameLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"chrStart.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"exonGeTrInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
"exonInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
"geneInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
"genomeParameters.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"sjdbInfo.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"sjdbList.fromGTF.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
"sjdbList.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
"transcriptInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"trans.blast.align_coords.align_coords.dat:md5,d41d8cd98f00b204e9800998ecf8427e",
"trans.blast.align_coords.align_coords.dbm:md5,d41d8cd98f00b204e9800998ecf8427e",
"trans.blast.dat.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
Expand All @@ -136,7 +178,31 @@
[
"AnnotFilterRule.pm:md5,d41d8cd98f00b204e9800998ecf8427e",
"PFAM.domtblout.dat.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
"__chkpts:md5,d41d8cd98f00b204e9800998ecf8427e",
[
"_fusion_annot_lib.idx.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"_prot_info_db.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"annotfiltrule_cp.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"blast_pairs.idx.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"cp_gene_blast_pairs.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"cp_pfam_dat.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"cp_ref_annot_cdna.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"fusion_annot_lib.cp.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"index_pfam_hits.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"index_ref_annot_cdna.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"makeblastdb.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"mm2.splice_bed.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"mm2_genome_idx.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"ref_annot.cdsplus.dfam_masked.fa.cp.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"ref_annot.cdsplus.dfam_masked.fa.idx.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"ref_annot.gtf.gene_spans.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"ref_annot.gtf.mini.sortu.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"ref_annot.gtf.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"ref_genome.fa.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"ref_genome_fai.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"trans.blast.dat.cp.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"trans.blast.dat.index.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"validate_ctat_genome_lib.ok:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"blast_pairs.dat.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
"blast_pairs.idx:md5,d41d8cd98f00b204e9800998ecf8427e",
"fusion_annot_lib.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
Expand Down Expand Up @@ -164,7 +230,25 @@
"ref_genome.fa.nsq:md5,d41d8cd98f00b204e9800998ecf8427e",
"ref_genome.fa.ntf:md5,d41d8cd98f00b204e9800998ecf8427e",
"ref_genome.fa.nto:md5,d41d8cd98f00b204e9800998ecf8427e",
"ref_genome.fa.star.idx:md5,d41d8cd98f00b204e9800998ecf8427e",
[
"Genome:md5,d41d8cd98f00b204e9800998ecf8427e",
"Log.out:md5,d41d8cd98f00b204e9800998ecf8427e",
"SA:md5,d41d8cd98f00b204e9800998ecf8427e",
"SAindex:md5,d41d8cd98f00b204e9800998ecf8427e",
"build.ok:md5,d41d8cd98f00b204e9800998ecf8427e",
"chrLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"chrName.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"chrNameLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"chrStart.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"exonGeTrInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
"exonInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
"geneInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
"genomeParameters.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"sjdbInfo.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"sjdbList.fromGTF.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
"sjdbList.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
"transcriptInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"trans.blast.align_coords.align_coords.dat:md5,d41d8cd98f00b204e9800998ecf8427e",
"trans.blast.align_coords.align_coords.dbm:md5,d41d8cd98f00b204e9800998ecf8427e",
"trans.blast.dat.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
Expand All @@ -177,6 +261,6 @@
"nf-test": "0.9.0",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-11T15:05:16.428455255"
"timestamp": "2024-12-12T14:57:33.861849482"
}
}
}

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