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remove dumpsoftwareversions and cleanup a bit sammyseq.nf
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@daisymut
daisymut committed Nov 8, 2024
1 parent 14c99fd commit 8bbb133
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Showing 11 changed files with 153 additions and 376 deletions.
8 changes: 0 additions & 8 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -26,14 +26,6 @@ process {
]
}

withName: CUSTOM_DUMPSOFTWAREVERSIONS {
publishDir = [
path: { "${params.outdir}/pipeline_info" },
mode: params.publish_dir_mode,
pattern: '*_versions.yml'
]
}

withName: 'MULTIQC' {
ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
publishDir = [
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106 changes: 76 additions & 30 deletions modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -8,97 +8,131 @@
"bwa/aln": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["fastq_align_bwaaln", "modules"]
"installed_by": [
"fastq_align_bwaaln",
"modules"
]
},
"bwa/index": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"bwa/sampe": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["fastq_align_bwaaln"]
"installed_by": [
"fastq_align_bwaaln"
]
},
"bwa/samse": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["fastq_align_bwaaln"]
"installed_by": [
"fastq_align_bwaaln"
]
},
"cat/fastq": {
"branch": "master",
"git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc",
"installed_by": ["modules"]
},
"custom/dumpsoftwareversions": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"deeptools/bamcoverage": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"fastqc": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"gunzip": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"multiqc": {
"branch": "master",
"git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"picard/markduplicates": {
"branch": "master",
"git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
"installed_by": ["bam_markduplicates_picard", "modules"]
"installed_by": [
"bam_markduplicates_picard",
"modules"
]
},
"samtools/faidx": {
"branch": "master",
"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"samtools/flagstat": {
"branch": "master",
"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
"installed_by": ["bam_stats_samtools"]
"installed_by": [
"bam_stats_samtools"
]
},
"samtools/idxstats": {
"branch": "master",
"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
"installed_by": ["bam_stats_samtools"]
"installed_by": [
"bam_stats_samtools"
]
},
"samtools/index": {
"branch": "master",
"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
"installed_by": ["bam_markduplicates_picard", "fastq_align_bwaaln"]
"installed_by": [
"bam_markduplicates_picard",
"fastq_align_bwaaln"
]
},
"samtools/stats": {
"branch": "master",
"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
"installed_by": ["bam_stats_samtools"]
"installed_by": [
"bam_stats_samtools"
]
},
"trimgalore": {
"branch": "master",
"git_sha": "8c5eeedd45e295fc9a4f164631da6a8b37e6b9c6",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"trimmomatic": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"untar": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
}
}
},
Expand All @@ -107,35 +141,47 @@
"bam_markduplicates_picard": {
"branch": "master",
"git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
"installed_by": ["subworkflows"]
"installed_by": [
"subworkflows"
]
},
"bam_stats_samtools": {
"branch": "master",
"git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d",
"installed_by": ["bam_markduplicates_picard"]
"installed_by": [
"bam_markduplicates_picard"
]
},
"fastq_align_bwaaln": {
"branch": "master",
"git_sha": "c60c14b285b89bdd0607e371417dadb80385ad6e",
"installed_by": ["subworkflows"]
"installed_by": [
"subworkflows"
]
},
"utils_nextflow_pipeline": {
"branch": "master",
"git_sha": "56372688d8979092cafbe0c5c3895b491166ca1c",
"installed_by": ["subworkflows"]
"installed_by": [
"subworkflows"
]
},
"utils_nfcore_pipeline": {
"branch": "master",
"git_sha": "1b6b9a3338d011367137808b49b923515080e3ba",
"installed_by": ["subworkflows"]
"installed_by": [
"subworkflows"
]
},
"utils_nfschema_plugin": {
"branch": "master",
"git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
"installed_by": ["subworkflows"]
"installed_by": [
"subworkflows"
]
}
}
}
}
}
}
}
5 changes: 0 additions & 5 deletions modules/nf-core/custom/dumpsoftwareversions/environment.yml
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24 changes: 0 additions & 24 deletions modules/nf-core/custom/dumpsoftwareversions/main.nf
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43 changes: 0 additions & 43 deletions modules/nf-core/custom/dumpsoftwareversions/meta.yml
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