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Merge branch 'dev' into fasta-filtering

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James A. Fellows Yates 2022-04-18 07:31:14 +02:00 committed by GitHub
commit 9c3c8f1f4e
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3 changed files with 11 additions and 13 deletions
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2
subworkflows/local/input_check.nf
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@ -45,7 +45,6 @@ def create_fastq_channel(LinkedHashMap row) {
meta.run_accession = row.run_accession meta.run_accession = row.run_accession
meta.instrument_platform = row.instrument_platform meta.instrument_platform = row.instrument_platform
meta.single_end = row.single_end.toBoolean() meta.single_end = row.single_end.toBoolean()
meta.is_fasta = false
// add path(s) of the fastq file(s) to the meta map // add path(s) of the fastq file(s) to the meta map
def fastq_meta = [] def fastq_meta = []
@ -76,7 +75,6 @@ def create_fasta_channel(LinkedHashMap row) {
meta.run_accession = row.run_accession meta.run_accession = row.run_accession
meta.instrument_platform = row.instrument_platform meta.instrument_platform = row.instrument_platform
meta.single_end = true meta.single_end = true
meta.is_fasta = true
def array = [] def array = []
if (!file(row.fasta).exists()) { if (!file(row.fasta).exists()) {

18
subworkflows/local/profiling.nf
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@ -76,19 +76,19 @@ workflow PROFILING {
ch_input_for_centrifuge = ch_input_for_profiling.centrifuge ch_input_for_centrifuge = ch_input_for_profiling.centrifuge
.filter{ .filter{
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 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
!it[0].is_fasta !it[0].is_fasta
}
.multiMap {
it ->
reads: [ it[0] + it[2], it[1] ]
db: it[3]
} }
.multiMap {
it ->
reads: [ it[0] + it[2], it[1] ]
db: it[3]
}
ch_input_for_metaphlan3 = ch_input_for_profiling.metaphlan3 ch_input_for_metaphlan3 = ch_input_for_profiling.metaphlan3
.filter{ .filter{
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 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
!it[0].is_fasta !it[0].is_fasta
} }
.multiMap { .multiMap {
it -> it ->

4
workflows/taxprofiler.nf
View file

@ -176,10 +176,10 @@ workflow TAXPROFILER {
[ meta, [ reads ].flatten() ] [ meta, [ reads ].flatten() ]
} }
.mix( INPUT_CHECK.out.fasta ) .mix( INPUT_CHECK.out.fasta )
} else { } else {
ch_reads_runmerged = ch_shortreads_hostremoved ch_reads_runmerged = ch_shortreads_hostremoved
.mix( ch_longreads_preprocessed ) .mix( ch_longreads_preprocessed, INPUT_CHECK.out.fasta )
.mix( INPUT_CHECK.out.fasta )
} }
/* /*