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https://github.com/MillironX/taxprofiler.git
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Fix porechop conflict
This commit is contained in:
parent
074d3ec204
commit
3faea8aac5
4 changed files with 13 additions and 14 deletions
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@ -141,9 +141,9 @@
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"branch": "master",
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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},
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},
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"porechop": {
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"porechop/porechop": {
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"branch": "master",
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "2a4e85eb81875a572bb58133e37f84ba3cc484d7"
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},
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},
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"prinseqplusplus": {
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"prinseqplusplus": {
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"branch": "master",
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"branch": "master",
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@ -1,4 +1,4 @@
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process PORECHOP {
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process PORECHOP_PORECHOP {
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tag "$meta.id"
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tag "$meta.id"
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label 'process_medium'
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label 'process_medium'
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@ -28,7 +28,6 @@ process PORECHOP {
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$args \\
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$args \\
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-o ${prefix}.fastq.gz \\
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-o ${prefix}.fastq.gz \\
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> ${prefix}.log
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> ${prefix}.log
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cat <<-END_VERSIONS > versions.yml
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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"${task.process}":
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porechop: \$( porechop --version )
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porechop: \$( porechop --version )
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@ -1,4 +1,4 @@
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name: porechop
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name: "porechop_porechop"
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description: Adapter removal and demultiplexing of Oxford Nanopore reads
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description: Adapter removal and demultiplexing of Oxford Nanopore reads
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keywords:
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keywords:
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- adapter
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- adapter
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@ -5,7 +5,7 @@
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include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/fastqc/main'
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include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/fastqc/main'
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include { FALCO as FALCO_PROCESSED } from '../../modules/nf-core/falco/main'
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include { FALCO as FALCO_PROCESSED } from '../../modules/nf-core/falco/main'
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include { PORECHOP } from '../../modules/nf-core/porechop/main'
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include { PORECHOP_PORECHOP } from '../../modules/nf-core/porechop/porechop/main'
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include { FILTLONG } from '../../modules/nf-core/filtlong/main'
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include { FILTLONG } from '../../modules/nf-core/filtlong/main'
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workflow LONGREAD_PREPROCESSING {
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workflow LONGREAD_PREPROCESSING {
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@ -17,9 +17,9 @@ workflow LONGREAD_PREPROCESSING {
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ch_multiqc_files = Channel.empty()
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ch_multiqc_files = Channel.empty()
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if ( !params.longread_qc_skipadaptertrim && params.longread_qc_skipqualityfilter) {
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if ( !params.longread_qc_skipadaptertrim && params.longread_qc_skipqualityfilter) {
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PORECHOP ( reads )
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PORECHOP_PORECHOP ( reads )
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ch_processed_reads = PORECHOP.out.reads
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ch_processed_reads = PORECHOP_PORECHOP.out.reads
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.map {
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.map {
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meta, reads ->
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meta, reads ->
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def meta_new = meta.clone()
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def meta_new = meta.clone()
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@ -27,8 +27,8 @@ workflow LONGREAD_PREPROCESSING {
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[ meta_new, reads ]
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[ meta_new, reads ]
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}
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}
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ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
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ch_versions = ch_versions.mix(PORECHOP_PORECHOP.out.versions.first())
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ch_multiqc_files = ch_multiqc_files.mix( PORECHOP.out.log )
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ch_multiqc_files = ch_multiqc_files.mix( PORECHOP_PORECHOP.out.log )
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} else if ( params.longread_qc_skipadaptertrim && !params.longread_qc_skipqualityfilter) {
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} else if ( params.longread_qc_skipadaptertrim && !params.longread_qc_skipqualityfilter) {
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@ -37,8 +37,8 @@ workflow LONGREAD_PREPROCESSING {
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ch_multiqc_files = ch_multiqc_files.mix( FILTLONG.out.log )
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ch_multiqc_files = ch_multiqc_files.mix( FILTLONG.out.log )
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} else {
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} else {
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PORECHOP ( reads )
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PORECHOP_PORECHOP ( reads )
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ch_clipped_reads = PORECHOP.out.reads
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ch_clipped_reads = PORECHOP_PORECHOP.out.reads
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.map {
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.map {
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meta, reads ->
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meta, reads ->
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def meta_new = meta.clone()
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def meta_new = meta.clone()
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@ -48,9 +48,9 @@ workflow LONGREAD_PREPROCESSING {
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ch_processed_reads = FILTLONG ( ch_clipped_reads.map{ meta, reads -> [meta, [], reads ]} ).reads
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ch_processed_reads = FILTLONG ( ch_clipped_reads.map{ meta, reads -> [meta, [], reads ]} ).reads
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ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
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ch_versions = ch_versions.mix(PORECHOP_PORECHOP.out.versions.first())
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ch_versions = ch_versions.mix(FILTLONG.out.versions.first())
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ch_versions = ch_versions.mix(FILTLONG.out.versions.first())
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ch_multiqc_files = ch_multiqc_files.mix( PORECHOP.out.log )
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ch_multiqc_files = ch_multiqc_files.mix( PORECHOP_PORECHOP.out.log )
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ch_multiqc_files = ch_multiqc_files.mix( FILTLONG.out.log )
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ch_multiqc_files = ch_multiqc_files.mix( FILTLONG.out.log )
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}
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}
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