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use custom container for fusioncatcher, fix typo
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@rannick
rannick committed Dec 17, 2024
1 parent f2bc314 commit 17ef233
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Showing 4 changed files with 19 additions and 188 deletions.
3 changes: 2 additions & 1 deletion modules/local/fusioncatcher/detect/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,8 @@ process FUSIONCATCHER {
label 'process_high'

conda "${moduleDir}/environment.yml"
container "community.wave.seqera.io/library/fusioncatcher:1.33--4733482b637ef92f"

container "docker.io/rannickscilifelab/fusioncatcher:1.34"

input:
tuple val(meta), path(fasta)
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2 changes: 1 addition & 1 deletion modules/local/fusioncatcher/download/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ process FUSIONCATCHER_DOWNLOAD {
label 'process_medium'

conda "${moduleDir}/environment.yml"
container "community.wave.seqera.io/library/fusioncatcher:1.33--4733482b637ef92f"
container "docker.io/rannickscilifelab/fusioncatcher:1.34"


input:
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198 changes: 14 additions & 184 deletions tests/test_stub.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,11 +1,8 @@
{
"stub test no fastp trim": {
"content": [
31,
20,
{
"ARRIBA_ARRIBA": {
"arriba": "2.4.0"
},
"ARRIBA_DOWNLOAD": {
"arriba_download": "2.4.0"
},
Expand All @@ -19,14 +16,11 @@
"fastqc": "0.12.1"
},
"FUSIONCATCHER": {
"fusioncatcher": 1.33
"fusioncatcher": 1.35
},
"FUSIONCATCHER_BUILD": {
"fusioncatcher": "fusioncatcher.py 1.35"
},
"FUSIONREPORT": {
"fusion_report": "2.1.5"
},
"FUSIONREPORT_DOWNLOAD": {
"fusion_report": "2.1.5"
},
Expand All @@ -36,10 +30,6 @@
"GATK4_CREATESEQUENCEDICTIONARY": {
"gatk4": "4.6.1.0"
},
"GATK4_MARKDUPLICATES": {
"gatk4": "4.5.0.0",
"samtools": "1.19.2"
},
"GENCODE_DOWNLOAD": {
"wget": null
},
Expand All @@ -55,59 +45,32 @@
"HGNC_DOWNLOAD": {
"wget": null
},
"PICARD_COLLECTINSERTSIZEMETRICS": {
"picard": "3.3.0"
},
"PICARD_COLLECTRNASEQMETRICS": {
"picard": "3.3.0"
},
"SALMON_INDEX": {
"salmon": "1.10.3"
},
"SALMON_QUANT": {
"salmon": "1.10.3"
},
"SAMTOOLS_FAIDX": {
"samtools": 1.21
},
"SAMTOOLS_INDEX_FOR_STARFUSION": {
"samtools": 1.21
},
"STARFUSION": {
"STAR-Fusion": "1.7.0"
},
"STARFUSION_BUILD": {
"STAR-Fusion": "1.7.0"
},
"STAR_FOR_ARRIBA": {
"star": "2.7.11b",
"star": null,
"samtools": 1.2,
"gawk": "5.1.0"
},
"STAR_FOR_STARFUSION": {
"star": "2.7.11b",
"star": null,
"samtools": 1.2,
"gawk": "5.1.0"
},
"STAR_GENOMEGENERATE": {
"star": "2.7.11b",
"star": null,
"samtools": 1.2,
"gawk": "5.1.0"
},
"STRINGTIE_MERGE": {
"stringtie": "2.2.1"
},
"STRINGTIE_STRINGTIE": {
"stringtie": "2.2.3"
},
"Workflow": {
"nf-core/rnafusion": "v4.0.0dev"
}
},
[
"arriba",
"arriba/test.arriba.fusions.discarded.tsv",
"arriba/test.arriba.fusions.tsv",
"fastp",
"fastp/test.fastp.html",
"fastp/test.fastp.json",
Expand All @@ -126,32 +89,11 @@
"fusioncatcher/test.fusioncatcher.fusion-genes.txt",
"fusioncatcher/test.fusioncatcher.log",
"fusioncatcher/test.fusioncatcher.summary.txt",
"fusionreport",
"fusionreport/test",
"fusionreport/test/AAA_BBB.html",
"fusionreport/test/test.fusionreport.tsv",
"fusionreport/test/test.fusionreport_filtered.tsv",
"fusionreport/test/test.fusions.csv",
"fusionreport/test/test.fusions.json",
"fusionreport/test/test_fusionreport_index.html",
"gatk4",
"gatk4/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict",
"get",
"get/rrna.bed",
"get/rrna.gtf",
"multiqc",
"multiqc/multiqc_data",
"multiqc/multiqc_plots",
"multiqc/multiqc_report.html",
"picard",
"picard/test.bai",
"picard/test.bam",
"picard/test.bam.metrics",
"picard/test.cram",
"picard/test.cram.crai",
"picard/test.rna_metrics",
"picard/test_collectinsertsize.pdf",
"picard/test_collectinsertsize.txt",
"pipeline_info",
"pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
"references",
Expand Down Expand Up @@ -214,10 +156,6 @@
"references/starfusion",
"references/starfusion/ctat_genome_lib_build_dir",
"references/starfusion/ref_annot.cdna.fa",
"salmon",
"salmon/test",
"salmon/test_lib_format_counts.json",
"salmon/test_meta_info.json",
"star_for_arriba",
"star_for_arriba/test.Aligned.sortedByCoord.out.bam",
"star_for_arriba/test.Aligned.unsort.out.bam",
Expand Down Expand Up @@ -249,38 +187,23 @@
"star_for_starfusion/test.Signal.UniqueMultiple.str1.out.wig",
"star_for_starfusion/test.out.sam",
"star_for_starfusion/test.sortedByCoord.out.bam",
"star_for_starfusion/test.sortedByCoord.out.bam.bai",
"star_for_starfusion/test.tab",
"star_for_starfusion/test.toTranscriptome.out.bam",
"star_for_starfusion/test.unmapped_1.fastq.gz",
"star_for_starfusion/test.unmapped_2.fastq.gz",
"star_for_starfusion/testXd.out.bam",
"starfusion",
"starfusion/test.starfusion.abridged.coding_effect.tsv",
"starfusion/test.starfusion.abridged.tsv",
"starfusion/test.starfusion.fusion_predictions.tsv",
"stringtie",
"stringtie/[:]",
"stringtie/[:]/stringtie.merged.gtf",
"stringtie/test.ballgown",
"stringtie/test.coverage.gtf",
"stringtie/test.gene.abundance.txt",
"stringtie/test.transcripts.gtf"
"star_for_starfusion/testXd.out.bam"
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-11T12:43:59.534889"
"timestamp": "2024-12-17T16:44:02.121512"
},
"stub test with fastp trim": {
"content": [
31,
19,
{
"ARRIBA_ARRIBA": {
"arriba": "2.4.0"
},
"ARRIBA_DOWNLOAD": {
"arriba_download": "2.4.0"
},
Expand All @@ -294,14 +217,11 @@
"fastqc": "0.12.1"
},
"FUSIONCATCHER": {
"fusioncatcher": 1.33
"fusioncatcher": 1.35
},
"FUSIONCATCHER_BUILD": {
"fusioncatcher": "fusioncatcher.py 1.35"
},
"FUSIONREPORT": {
"fusion_report": "2.1.5"
},
"FUSIONREPORT_DOWNLOAD": {
"fusion_report": "2.1.5"
},
Expand All @@ -311,10 +231,6 @@
"GATK4_CREATESEQUENCEDICTIONARY": {
"gatk4": "4.6.1.0"
},
"GATK4_MARKDUPLICATES": {
"gatk4": "4.5.0.0",
"samtools": "1.19.2"
},
"GENCODE_DOWNLOAD": {
"wget": null
},
Expand All @@ -330,59 +246,27 @@
"HGNC_DOWNLOAD": {
"wget": null
},
"PICARD_COLLECTINSERTSIZEMETRICS": {
"picard": "3.3.0"
},
"PICARD_COLLECTRNASEQMETRICS": {
"picard": "3.3.0"
},
"SALMON_INDEX": {
"salmon": "1.10.3"
},
"SALMON_QUANT": {
"salmon": "1.10.3"
},
"SAMTOOLS_FAIDX": {
"samtools": 1.21
},
"SAMTOOLS_INDEX_FOR_STARFUSION": {
"samtools": 1.21
},
"STARFUSION": {
"STAR-Fusion": "1.7.0"
},
"STARFUSION_BUILD": {
"STAR-Fusion": "1.7.0"
},
"STAR_FOR_ARRIBA": {
"star": "2.7.11b",
"samtools": 1.2,
"gawk": "5.1.0"
},
"STAR_FOR_STARFUSION": {
"star": "2.7.11b",
"star": null,
"samtools": 1.2,
"gawk": "5.1.0"
},
"STAR_GENOMEGENERATE": {
"star": "2.7.11b",
"star": null,
"samtools": 1.2,
"gawk": "5.1.0"
},
"STRINGTIE_MERGE": {
"stringtie": "2.2.1"
},
"STRINGTIE_STRINGTIE": {
"stringtie": "2.2.3"
},
"Workflow": {
"nf-core/rnafusion": "v4.0.0dev"
}
},
[
"arriba",
"arriba/test.arriba.fusions.discarded.tsv",
"arriba/test.arriba.fusions.tsv",
"fastp",
"fastp/test.fastp.html",
"fastp/test.fastp.json",
Expand All @@ -401,32 +285,11 @@
"fusioncatcher/test.fusioncatcher.fusion-genes.txt",
"fusioncatcher/test.fusioncatcher.log",
"fusioncatcher/test.fusioncatcher.summary.txt",
"fusionreport",
"fusionreport/test",
"fusionreport/test/AAA_BBB.html",
"fusionreport/test/test.fusionreport.tsv",
"fusionreport/test/test.fusionreport_filtered.tsv",
"fusionreport/test/test.fusions.csv",
"fusionreport/test/test.fusions.json",
"fusionreport/test/test_fusionreport_index.html",
"gatk4",
"gatk4/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict",
"get",
"get/rrna.bed",
"get/rrna.gtf",
"multiqc",
"multiqc/multiqc_data",
"multiqc/multiqc_plots",
"multiqc/multiqc_report.html",
"picard",
"picard/test.bai",
"picard/test.bam",
"picard/test.bam.metrics",
"picard/test.cram",
"picard/test.cram.crai",
"picard/test.rna_metrics",
"picard/test_collectinsertsize.pdf",
"picard/test_collectinsertsize.txt",
"pipeline_info",
"pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
"references",
Expand All @@ -452,23 +315,6 @@
"references/hgnc",
"references/hgnc/HGNC-DB-timestamp.txt",
"references/hgnc/hgnc_complete_set.txt",
"references/salmon",
"references/salmon/salmon",
"references/salmon/salmon/complete_ref_lens.bin",
"references/salmon/salmon/ctable.bin",
"references/salmon/salmon/ctg_offsets.bin",
"references/salmon/salmon/duplicate_clusters.tsv",
"references/salmon/salmon/info.json",
"references/salmon/salmon/mphf.bin",
"references/salmon/salmon/pos.bin",
"references/salmon/salmon/pre_indexing.log",
"references/salmon/salmon/rank.bin",
"references/salmon/salmon/refAccumLengths.bin",
"references/salmon/salmon/ref_indexing.log",
"references/salmon/salmon/reflengths.bin",
"references/salmon/salmon/refseq.bin",
"references/salmon/salmon/seq.bin",
"references/salmon/salmon/versionInfo.json",
"references/star",
"references/star/Genome",
"references/star/Log.out",
Expand All @@ -489,10 +335,6 @@
"references/starfusion",
"references/starfusion/ctat_genome_lib_build_dir",
"references/starfusion/ref_annot.cdna.fa",
"salmon",
"salmon/test",
"salmon/test_lib_format_counts.json",
"salmon/test_meta_info.json",
"star_for_arriba",
"star_for_arriba/test.Aligned.sortedByCoord.out.bam",
"star_for_arriba/test.Aligned.unsort.out.bam",
Expand Down Expand Up @@ -524,29 +366,17 @@
"star_for_starfusion/test.Signal.UniqueMultiple.str1.out.wig",
"star_for_starfusion/test.out.sam",
"star_for_starfusion/test.sortedByCoord.out.bam",
"star_for_starfusion/test.sortedByCoord.out.bam.bai",
"star_for_starfusion/test.tab",
"star_for_starfusion/test.toTranscriptome.out.bam",
"star_for_starfusion/test.unmapped_1.fastq.gz",
"star_for_starfusion/test.unmapped_2.fastq.gz",
"star_for_starfusion/testXd.out.bam",
"starfusion",
"starfusion/test.starfusion.abridged.coding_effect.tsv",
"starfusion/test.starfusion.abridged.tsv",
"starfusion/test.starfusion.fusion_predictions.tsv",
"stringtie",
"stringtie/[:]",
"stringtie/[:]/stringtie.merged.gtf",
"stringtie/test.ballgown",
"stringtie/test.coverage.gtf",
"stringtie/test.gene.abundance.txt",
"stringtie/test.transcripts.gtf"
"star_for_starfusion/testXd.out.bam"
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-11T12:40:22.066494"
"timestamp": "2024-12-17T16:42:11.182735"
}
}
}
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