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Merge branch 'dev' into fasta-filtering
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commit
9c3c8f1f4e
3 changed files with 11 additions and 13 deletions
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@ -45,7 +45,6 @@ def create_fastq_channel(LinkedHashMap row) {
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meta.run_accession = row.run_accession
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meta.instrument_platform = row.instrument_platform
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meta.single_end = row.single_end.toBoolean()
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meta.is_fasta = false
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// add path(s) of the fastq file(s) to the meta map
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def fastq_meta = []
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@ -76,7 +75,6 @@ def create_fasta_channel(LinkedHashMap row) {
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meta.run_accession = row.run_accession
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meta.instrument_platform = row.instrument_platform
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meta.single_end = true
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meta.is_fasta = true
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def array = []
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if (!file(row.fasta).exists()) {
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@ -76,19 +76,19 @@ workflow PROFILING {
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ch_input_for_centrifuge = ch_input_for_profiling.centrifuge
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.filter{
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if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] Centrifuge currently does not accept FASTA files as input. Skipping Centrifuge for sample " + it[0].id
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!it[0].is_fasta
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if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] Centrifuge currently does not accept FASTA files as input. Skipping Centrifuge for sample " + it[0].id
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!it[0].is_fasta
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}
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.multiMap {
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it ->
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reads: [ it[0] + it[2], it[1] ]
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db: it[3]
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}
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.multiMap {
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it ->
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reads: [ it[0] + it[2], it[1] ]
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db: it[3]
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}
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ch_input_for_metaphlan3 = ch_input_for_profiling.metaphlan3
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.filter{
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if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] MetaPhlAn3 does not accept FASTA files as input. Skipping MetaPhlAn3 for sample " + it[0].id
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!it[0].is_fasta
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if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] Centrifuge currently does not accept FASTA files as input. Skipping Centrifuge for sample " + it[0].id
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!it[0].is_fasta
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}
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.multiMap {
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it ->
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@ -176,10 +176,10 @@ workflow TAXPROFILER {
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[ meta, [ reads ].flatten() ]
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}
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.mix( INPUT_CHECK.out.fasta )
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} else {
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ch_reads_runmerged = ch_shortreads_hostremoved
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.mix( ch_longreads_preprocessed )
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.mix( INPUT_CHECK.out.fasta )
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.mix( ch_longreads_preprocessed, INPUT_CHECK.out.fasta )
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}
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/*
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