millironx/taxprofiler
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Merge pull request #66 from nf-core/versions-fix

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Fix version reporting
This commit is contained in:
James A. Fellows Yates 2022-04-25 16:38:28 +02:00 committed by GitHub
commit bc84afe80d
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3 changed files with 8 additions and 13 deletions
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2
subworkflows/local/db_check.nf
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@ -34,7 +34,7 @@ workflow DB_CHECK {
emit: emit:
dbs = ch_final_dbs // channel: [ val(meta), [ db ] ] dbs = ch_final_dbs // channel: [ val(meta), [ db ] ]
versions = DATABASE_CHECK.out.versions // channel: [ versions.yml ] versions = DATABASE_CHECK.out.versions.mix(UNTAR.out.versions.first()) // channel: [ versions.yml ]
} }
def create_db_channels(LinkedHashMap row) { def create_db_channels(LinkedHashMap row) {

2
subworkflows/local/profiling.nf
View file

@ -130,7 +130,7 @@ workflow PROFILING {
MEGAN_RMA2INFO (ch_maltrun_for_megan, params.malt_generatemegansummary ) MEGAN_RMA2INFO (ch_maltrun_for_megan, params.malt_generatemegansummary )
ch_multiqc_files = ch_multiqc_files.mix( MALT_RUN.out.log.collect{it[1]}.ifEmpty([]) ) ch_multiqc_files = ch_multiqc_files.mix( MALT_RUN.out.log.collect{it[1]}.ifEmpty([]) )
ch_versions = ch_versions.mix( MALT_RUN.out.versions.first() ) ch_versions = ch_versions.mix( MALT_RUN.out.versions.first(), MEGAN_RMA2INFO.out.versions.first() )
ch_raw_profiles = ch_raw_profiles.mix( MEGAN_RMA2INFO.out.txt ) ch_raw_profiles = ch_raw_profiles.mix( MEGAN_RMA2INFO.out.txt )
} }

17
workflows/taxprofiler.nf
View file

@ -111,8 +111,8 @@ workflow TAXPROFILER {
SUBWORKFLOW: PERFORM PREPROCESSING SUBWORKFLOW: PERFORM PREPROCESSING
*/ */
if ( params.perform_shortread_clipmerge ) { if ( params.perform_shortread_clipmerge ) {
ch_shortreads_preprocessed = SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq ).reads ch_shortreads_preprocessed = SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq ).reads
ch_versions = ch_versions.mix( SHORTREAD_PREPROCESSING.out.versions )
} else { } else {
ch_shortreads_preprocessed = INPUT_CHECK.out.fastq ch_shortreads_preprocessed = INPUT_CHECK.out.fastq
} }
@ -120,7 +120,7 @@ workflow TAXPROFILER {
if ( params.perform_longread_clip ) { if ( params.perform_longread_clip ) {
ch_longreads_preprocessed = LONGREAD_PREPROCESSING ( INPUT_CHECK.out.nanopore ).reads ch_longreads_preprocessed = LONGREAD_PREPROCESSING ( INPUT_CHECK.out.nanopore ).reads
.map { it -> [ it[0], [it[1]] ] } .map { it -> [ it[0], [it[1]] ] }
ch_versions = ch_versions.mix(LONGREAD_PREPROCESSING.out.versions.first()) ch_versions = ch_versions.mix( LONGREAD_PREPROCESSING.out.versions )
} else { } else {
ch_longreads_preprocessed = INPUT_CHECK.out.nanopore ch_longreads_preprocessed = INPUT_CHECK.out.nanopore
} }
@ -131,6 +131,7 @@ workflow TAXPROFILER {
if ( params.perform_shortread_complexityfilter ) { if ( params.perform_shortread_complexityfilter ) {
ch_shortreads_filtered = SHORTREAD_COMPLEXITYFILTERING ( ch_shortreads_preprocessed ).reads ch_shortreads_filtered = SHORTREAD_COMPLEXITYFILTERING ( ch_shortreads_preprocessed ).reads
ch_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions )
} else { } else {
ch_shortreads_filtered = ch_shortreads_preprocessed ch_shortreads_filtered = ch_shortreads_preprocessed
} }
@ -141,7 +142,7 @@ workflow TAXPROFILER {
if ( params.perform_shortread_hostremoval ) { if ( params.perform_shortread_hostremoval ) {
ch_shortreads_hostremoved = SHORTREAD_HOSTREMOVAL ( ch_shortreads_filtered, ch_reference, ch_reference_index ).reads ch_shortreads_hostremoved = SHORTREAD_HOSTREMOVAL ( ch_shortreads_filtered, ch_reference, ch_reference_index ).reads
ch_versions = ch_versions.mix(SHORTREAD_HOSTREMOVAL.out.versions.first()) ch_versions = ch_versions.mix(SHORTREAD_HOSTREMOVAL.out.versions)
} else { } else {
ch_shortreads_hostremoved = ch_shortreads_filtered ch_shortreads_hostremoved = ch_shortreads_filtered
} }
@ -177,6 +178,8 @@ workflow TAXPROFILER {
} }
.mix( INPUT_CHECK.out.fasta ) .mix( INPUT_CHECK.out.fasta )
ch_versions = ch_versions.mix(CAT_FASTQ.out.versions)
} else { } else {
ch_reads_runmerged = ch_shortreads_hostremoved ch_reads_runmerged = ch_shortreads_hostremoved
.mix( ch_longreads_preprocessed, INPUT_CHECK.out.fasta ) .mix( ch_longreads_preprocessed, INPUT_CHECK.out.fasta )
@ -210,26 +213,18 @@ workflow TAXPROFILER {
if (params.perform_shortread_clipmerge) { if (params.perform_shortread_clipmerge) {
ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) ) ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
ch_versions = ch_versions.mix( SHORTREAD_PREPROCESSING.out.versions )
} }
if (params.perform_longread_clip) { if (params.perform_longread_clip) {
ch_multiqc_files = ch_multiqc_files.mix( LONGREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) ) ch_multiqc_files = ch_multiqc_files.mix( LONGREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
ch_versions = ch_versions.mix( LONGREAD_PREPROCESSING.out.versions )
} }
if (params.perform_shortread_complexityfilter){ if (params.perform_shortread_complexityfilter){
ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_COMPLEXITYFILTERING.out.mqc.collect{it[1]}.ifEmpty([]) ) ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_COMPLEXITYFILTERING.out.mqc.collect{it[1]}.ifEmpty([]) )
ch_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions )
} }
if (params.perform_shortread_hostremoval) { if (params.perform_shortread_hostremoval) {
ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_HOSTREMOVAL.out.mqc.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_HOSTREMOVAL.out.mqc.collect{it[1]}.ifEmpty([]))
ch_versions = ch_versions.mix(SHORTREAD_HOSTREMOVAL.out.versions)
}
if (params.perform_runmerging){
ch_versions = ch_versions.mix(CAT_FASTQ.out.versions)
} }
ch_multiqc_files = ch_multiqc_files.mix( PROFILING.out.mqc ) ch_multiqc_files = ch_multiqc_files.mix( PROFILING.out.mqc )