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Adds filtering and warning for non-FASTA supporting tool. Standardised warning messages.

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This commit is contained in:
James Fellows Yates 2022-04-18 07:21:12 +02:00
parent fc8a83245a
commit 564474cafe
3 changed files with 16 additions and 5 deletions
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2
subworkflows/local/input_check.nf
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@ -45,6 +45,7 @@ def create_fastq_channel(LinkedHashMap row) {
meta.run_accession = row.run_accession
meta.instrument_platform = row.instrument_platform
meta.single_end = row.single_end.toBoolean()
meta.is_fasta = false
// add path(s) of the fastq file(s) to the meta map
def fastq_meta = []
@ -75,6 +76,7 @@ def create_fasta_channel(LinkedHashMap row) {
meta.run_accession = row.run_accession
meta.instrument_platform = row.instrument_platform
meta.single_end = true
meta.is_fasta = true
def array = []
if (!file(row.fasta).exists()) {

8
subworkflows/local/profiling.nf
View file

@ -75,6 +75,10 @@ workflow PROFILING {
}
ch_input_for_centrifuge = ch_input_for_profiling.centrifuge
.filter{
if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] Centrifuge does not accept FASTA files as input. Skipping Centrifuge for sample " + it[0].id
!it[0].is_fasta
}
.multiMap {
it ->
reads: [ it[0] + it[2], it[1] ]
@ -82,6 +86,10 @@ workflow PROFILING {
}
ch_input_for_metaphlan3 = ch_input_for_profiling.metaphlan3
.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
!it[0].is_fasta
}
.multiMap {
it ->
reads: [it[0] + it[2], it[1]]

11
workflows/taxprofiler.nf
View file

@ -19,11 +19,11 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true
// Check mandatory parameters
if (params.input ) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
if (params.shortread_clipmerge_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] warning: MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
if (params.shortread_clipmerge_excludeunmerged && !params.shortread_clipmerge_mergepairs) exit 1, "[nf-core/taxprofiler] error: cannot include unmerged reads when merging not turned on. Please specify --shortread_clipmerge_mergepairs"
if (params.shortread_clipmerge_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler]: MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
if (params.shortread_clipmerge_excludeunmerged && !params.shortread_clipmerge_mergepairs) exit 1, "ERROR: [nf-core/taxprofiler] cannot include unmerged reads when merging not turned on. Please specify --shortread_clipmerge_mergepairs"
if (params.perform_shortread_hostremoval && !params.shortread_hostremoval_reference) { exit 1, "[nf-core/taxprofiler] error: --shortread_hostremoval requested but no --shortread_hostremoval_reference FASTA supplied. Check input." }
if (!params.shortread_hostremoval_reference && params.shortread_hostremoval_reference_index) { exit 1, "[nf-core/taxprofiler] error: --shortread_hostremoval_index provided but no --shortread_hostremoval_reference FASTA supplied. Check input." }
if (params.perform_shortread_hostremoval && !params.shortread_hostremoval_reference) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval requested but no --shortread_hostremoval_reference FASTA supplied. Check input." }
if (!params.shortread_hostremoval_reference && params.shortread_hostremoval_reference_index) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval_index provided but no --shortread_hostremoval_reference FASTA supplied. Check input." }
if (params.shortread_hostremoval_reference ) { ch_reference = file(params.shortread_hostremoval_reference) }
if (params.shortread_hostremoval_index ) { ch_reference_index = file(params.shortread_hostremoval_index ) } else { ch_reference_index = [] }
@ -175,10 +175,11 @@ workflow TAXPROFILER {
meta, reads ->
[ meta, [ reads ].flatten() ]
}
.mix( INPUT_CHECK.out.fasta )
} else {
ch_reads_runmerged = ch_shortreads_hostremoved
.mix( ch_longreads_preprocessed )
.mix( INPUT_CHECK.out.fasta )
}
/*