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nf-core modules update --all #420

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merged 3 commits into from
Aug 4, 2021
Merged

nf-core modules update --all #420

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0bcdd72
feat: nf-core modules update --all
maxulysse Aug 4, 2021
3812485
fix: code polishing
maxulysse Aug 4, 2021
abe359b
fix: revert to old tabix version
maxulysse Aug 4, 2021
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12 changes: 6 additions & 6 deletions modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -19,16 +19,16 @@
"git_sha": "c8877835c288eb32b2ad1810d38a78e83e791f3d"
},
"multiqc": {
"git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
"git_sha": "c5235a983d454787fa0c3247b02086969217163b"
},
"samtools/faidx": {
"git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
"git_sha": "c5235a983d454787fa0c3247b02086969217163b"
},
"samtools/merge": {
"git_sha": "adfb8a3d6541f363aec83df16df873cbb767b388"
"git_sha": "c5235a983d454787fa0c3247b02086969217163b"
},
"seqkit/split2": {
"git_sha": "65ab646870c4ff74322b4fff22ad51b190791a2c"
"git_sha": "c5235a983d454787fa0c3247b02086969217163b"
},
"snpeff": {
"git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
Expand All @@ -40,8 +40,8 @@
"git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
},
"trimgalore": {
"git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
"git_sha": "c5235a983d454787fa0c3247b02086969217163b"
}
}
}
}
}
6 changes: 3 additions & 3 deletions modules/nf-core/modules/multiqc/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -10,11 +10,11 @@ process MULTIQC {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }

conda (params.enable_conda ? "bioconda::multiqc=1.10.1" : null)
conda (params.enable_conda ? 'bioconda::multiqc=1.11' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/multiqc:1.10.1--py_0"
container "https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0"
} else {
container "quay.io/biocontainers/multiqc:1.10.1--py_0"
container "quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0"
}

input:
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6 changes: 3 additions & 3 deletions modules/nf-core/modules/samtools/faidx/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -11,11 +11,11 @@ process SAMTOOLS_FAIDX {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }

conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
} else {
container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
}

input:
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6 changes: 3 additions & 3 deletions modules/nf-core/modules/samtools/merge/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -11,11 +11,11 @@ process SAMTOOLS_MERGE {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }

conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
} else {
container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
}

input:
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6 changes: 3 additions & 3 deletions modules/nf-core/modules/seqkit/split2/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -12,12 +12,12 @@ process SEQKIT_SPLIT2 {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }

conda (params.enable_conda ? "bioconda::seqkit=0.16.0" : null)
conda (params.enable_conda ? 'bioconda::seqkit=0.16.1' : null)

if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/seqkit:0.16.0--h9ee0642_0"
container "https://depot.galaxyproject.org/singularity/seqkit:0.16.1--h9ee0642_0"
} else {
container "quay.io/biocontainers/seqkit:0.16.0--h9ee0642_0"
container "quay.io/biocontainers/seqkit:0.16.1--h9ee0642_0"
}

input:
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6 changes: 3 additions & 3 deletions modules/nf-core/modules/trimgalore/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -11,11 +11,11 @@ process TRIMGALORE {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }

conda (params.enable_conda ? "bioconda::trim-galore=0.6.6" : null)
conda (params.enable_conda ? 'bioconda::trim-galore=0.6.7' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/trim-galore:0.6.6--0"
container "https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0"
} else {
container "quay.io/biocontainers/trim-galore:0.6.6--0"
container "quay.io/biocontainers/trim-galore:0.6.7--hdfd78af_0"
}

input:
Expand Down
64 changes: 32 additions & 32 deletions subworkflows/local/build_indices.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -19,18 +19,18 @@ params.tabix_pon_options = [:]

// Initialize channels based on params or indices that were just built

include { BUILD_INTERVALS } from '../../modules/local/build_intervals/main' addParams(options: params.build_intervals_options)
include { BWA_INDEX as BWAMEM1_INDEX } from '../../modules/nf-core/modules/bwa/index/main' addParams(options: params.bwa_index_options)
include { BWAMEM2_INDEX } from '../../modules/nf-core/modules/bwamem2/index/main' addParams(options: params.bwamem2_index_options)
include { CREATE_INTERVALS_BED } from '../../modules/local/create_intervals_bed/main' addParams(options: params.create_intervals_bed_options)
include { GATK4_CREATESEQUENCEDICTIONARY as GATK4_DICT } from '../../modules/nf-core/modules/gatk4/createsequencedictionary/main' addParams(options: params.gatk4_dict_options)
include { MSISENSORPRO_SCAN } from '../../modules/local/msisensorpro/scan/main' addParams(options: params.msisensorpro_scan_options)
include { SAMTOOLS_FAIDX } from '../../modules/nf-core/modules/samtools/faidx/main' addParams(options: params.samtools_faidx_options)
include { TABIX_BGZIPTABIX } from '../../modules/nf-core/modules/tabix/bgziptabix/main' addParams(options: params.bgziptabix_options)
include { TABIX_TABIX as TABIX_DBSNP } from '../../modules/nf-core/modules/tabix/tabix/main' addParams(options: params.tabix_dbsnp_options)
include { TABIX_TABIX as TABIX_GERMLINE_RESOURCE } from '../../modules/nf-core/modules/tabix/tabix/main' addParams(options: params.tabix_germline_resource_options)
include { TABIX_TABIX as TABIX_KNOWN_INDELS } from '../../modules/nf-core/modules/tabix/tabix/main' addParams(options: params.tabix_known_indels_options)
include { TABIX_TABIX as TABIX_PON } from '../../modules/nf-core/modules/tabix/tabix/main' addParams(options: params.tabix_pon_options)
include { BUILD_INTERVALS } from '../../modules/local/build_intervals/main' addParams(options: params.build_intervals_options)
include { BWA_INDEX as BWAMEM1_INDEX } from '../../modules/nf-core/modules/bwa/index/main' addParams(options: params.bwa_index_options)
include { BWAMEM2_INDEX } from '../../modules/nf-core/modules/bwamem2/index/main' addParams(options: params.bwamem2_index_options)
include { CREATE_INTERVALS_BED } from '../../modules/local/create_intervals_bed/main' addParams(options: params.create_intervals_bed_options)
include { GATK4_CREATESEQUENCEDICTIONARY } from '../../modules/nf-core/modules/gatk4/createsequencedictionary/main' addParams(options: params.gatk4_dict_options)
include { MSISENSORPRO_SCAN } from '../../modules/local/msisensorpro/scan/main' addParams(options: params.msisensorpro_scan_options)
include { SAMTOOLS_FAIDX } from '../../modules/nf-core/modules/samtools/faidx/main' addParams(options: params.samtools_faidx_options)
include { TABIX_BGZIPTABIX } from '../../modules/nf-core/modules/tabix/bgziptabix/main' addParams(options: params.bgziptabix_options)
include { TABIX_TABIX as TABIX_DBSNP } from '../../modules/nf-core/modules/tabix/tabix/main' addParams(options: params.tabix_dbsnp_options)
include { TABIX_TABIX as TABIX_GERMLINE_RESOURCE } from '../../modules/nf-core/modules/tabix/tabix/main' addParams(options: params.tabix_germline_resource_options)
include { TABIX_TABIX as TABIX_KNOWN_INDELS } from '../../modules/nf-core/modules/tabix/tabix/main' addParams(options: params.tabix_known_indels_options)
include { TABIX_TABIX as TABIX_PON } from '../../modules/nf-core/modules/tabix/tabix/main' addParams(options: params.tabix_pon_options)

workflow BUILD_INDICES {
take:
Expand All @@ -52,64 +52,64 @@ workflow BUILD_INDICES {
if (params.aligner == "bwa-mem") (result_bwa, version_bwa) = BWAMEM1_INDEX(fasta)
else (result_bwa, version_bwa) = BWAMEM2_INDEX(fasta)

result_dict = Channel.empty()
result_dict = Channel.empty()
version_dict = Channel.empty()
if (!(params.dict) && !('annotate' in step) && !('controlfreec' in step))
(result_dict, version_dict) = GATK4_DICT(fasta)
(result_dict, version_dict) = GATK4_CREATESEQUENCEDICTIONARY(fasta)

result_fai = Channel.empty()
if (fasta_fai) result_fai = fasta_fai
result_fai = Channel.empty()
version_fai = Channel.empty()
if (fasta_fai) result_fai = fasta_fai
if (!(params.fasta_fai) && !('annotate' in step))
(result_fai, version_fai) = SAMTOOLS_FAIDX(fasta)

result_dbsnp_tbi = Channel.empty()
result_dbsnp_tbi = Channel.empty()
version_dbsnp_tbi = Channel.empty()
if (!(params.dbsnp_tbi) && params.dbsnp && ('mapping' in step || 'preparerecalibration' in step || 'controlfreec' in tools || 'haplotypecaller' in tools|| 'mutect2' in tools || 'tnscope' in tools)) {
dbsnp_id = dbsnp.map {it -> [[id:"$it.baseName"], it]}
dbsnp_id = dbsnp.map{ it -> [[id:it[0].baseName], it] }
(result_dbsnp_tbi, version_dbsnp_tbi) = TABIX_DBSNP(dbsnp_id)
result_dbsnp_tbi = result_dbsnp_tbi.map {meta, tbi -> [tbi]}
result_dbsnp_tbi = result_dbsnp_tbi.map{ meta, tbi -> [tbi] }
}

result_target_bed = Channel.empty()
result_target_bed = Channel.empty()
version_target_bed = Channel.empty()
if ((params.target_bed) && ('manta' in tools || 'strelka' in tools)) {
target_bed_id = target_bed.map {it -> [[id:"$it.baseName"], it]}
target_bed_id = target_bed.map{ it -> [[id:it[0].baseName], it] }
(result_target_bed, version_target_bed) = TABIX_BGZIPTABIX(target_bed_id)
result_target_bed = result_target_bed.map {meta, bed, tbi -> [bed, tbi]}
result_target_bed = result_target_bed.map{ meta, bed, tbi -> [bed, tbi] }
}

result_germline_resource_tbi = Channel.empty()
result_germline_resource_tbi = Channel.empty()
version_germline_resource_tbi = Channel.empty()
if (!(params.germline_resource_tbi) && params.germline_resource && 'mutect2' in tools) {
germline_resource_id = germline_resource.map {it -> [[id:"$it.baseName"], it]}
germline_resource_id = germline_resource.map{ it -> [[id:it[0].baseName], it] }
(result_germline_resource_tbi, version_germline_resource_tbi) = TABIX_GERMLINE_RESOURCE(germline_resource_id)
}

result_known_indels_tbi = Channel.empty()
result_known_indels_tbi = Channel.empty()
version_known_indels_tbi = Channel.empty()
if (!(params.known_indels_tbi) && params.known_indels && ('mapping' in step || 'preparerecalibration' in step)) {
known_indels_id = known_indels.map {it -> [[id:"$it.baseName"], it]}
known_indels_id = known_indels.map{ it -> [[id:it[0].baseName], it] }
(result_known_indels_tbi, version_known_indels_tbi) = TABIX_KNOWN_INDELS(known_indels_id)
result_known_indels_tbi = result_known_indels_tbi.map {meta, tbi -> [tbi]}
result_known_indels_tbi = result_known_indels_tbi.map{ meta, tbi -> [tbi] }
}

result_msisensorpro_scan = Channel.empty()
result_msisensorpro_scan = Channel.empty()
version_msisensorpro_scan = Channel.empty()
if ('msisensorpro' in tools)
(result_msisensorpro_scan, version_msisensorpro_scan) = MSISENSORPRO_SCAN(fasta)

result_pon_tbi = Channel.empty()
result_pon_tbi = Channel.empty()
version_pon_tbi = Channel.empty()
if (!(params.pon_tbi) && params.pon && ('tnscope' in tools || 'mutect2' in tools)) {
pon_id = pon.map {it -> [[id:"$it.baseName"], it]}
pon_id = pon.map{ it -> [[id:it[0].baseName], it] }
(result_pon_tbi, version_pon_tbi) = TABIX_PON(pon_id)
}

result_intervals = Channel.empty()
if (params.no_intervals) {
file("${params.outdir}/no_intervals.bed").text = "no_intervals\n"
result_intervals = Channel.from(file("${params.outdir}/no_intervals.bed"))
result_intervals = Channel.fromPath(file("${params.outdir}/no_intervals.bed"))
} else if (!('annotate' in step) && !('controlfreec' in step))
if (!params.intervals)
result_intervals = CREATE_INTERVALS_BED(BUILD_INTERVALS(result_fai))
Expand All @@ -118,7 +118,7 @@ workflow BUILD_INDICES {

if (!params.no_intervals) {
result_intervals = result_intervals.flatten()
.map { intervalFile ->
.map{ intervalFile ->
def duration = 0.0
for (line in intervalFile.readLines()) {
final fields = line.split('\t')
Expand Down