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Append pairment to ID at profiling to prevent multiqc-level filename crash

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This commit is contained in:
James Fellows Yates 2022-04-08 21:36:59 +02:00
parent 8839fe22b8
commit afb66e445f
1 changed files with 8 additions and 5 deletions
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13
workflows/taxprofiler.nf
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@ -147,8 +147,6 @@ workflow TAXPROFILER {
skip: true skip: true
} }
ch_reads_for_cat_branch.cat.dump(tag: "for_catting")
ch_reads_runmerged = CAT_FASTQ ( ch_reads_for_cat_branch.cat ).reads ch_reads_runmerged = CAT_FASTQ ( ch_reads_for_cat_branch.cat ).reads
.mix( ch_reads_for_cat_branch.skip ) .mix( ch_reads_for_cat_branch.skip )
.map { .map {
@ -157,8 +155,6 @@ workflow TAXPROFILER {
[ meta, [ reads ].flatten() ] [ meta, [ reads ].flatten() ]
} }
ch_reads_runmerged.dump(tag: "ch_reads_runmerged" )
} else { } else {
ch_reads_runmerged = ch_shortreads_filtered ch_reads_runmerged = ch_shortreads_filtered
.mix( ch_longreads_preprocessed ) .mix( ch_longreads_preprocessed )
@ -168,8 +164,15 @@ workflow TAXPROFILER {
COMBINE READS WITH POSSIBLE DATABASES COMBINE READS WITH POSSIBLE DATABASES
*/ */
// e.g. output [DUMP: reads_plus_db] [['id':'2612', 'run_accession':'combined', 'instrument_platform':'ILLUMINA', 'single_end':1], <reads_path>/2612.merged.fastq.gz, ['tool':'malt', 'db_name':'mal95', 'db_params':'"-id 90"'], <db_path>/malt90] // e.g. output [DUMP: reads_plus_db] [['id':'2612', 'run_accession':'combined', 'instrument_platform':'ILLUMINA', 'single_end':1], [ <reads_path>/2612.merged.fastq.gz ], ['tool':'malt', 'db_name':'mal95', 'db_params':'"-id 90"'], <db_path>/malt90]
ch_input_for_profiling = ch_reads_runmerged ch_input_for_profiling = ch_reads_runmerged
.map {
meta, reads ->
def meta_new = meta.clone()
pairtype = meta_new['single_end'] ? '_se' : '_pe'
meta_new['id'] = meta_new['id'] + pairtype
[meta_new, reads]
}
.combine(DB_CHECK.out.dbs) .combine(DB_CHECK.out.dbs)
.branch { .branch {
malt: it[2]['tool'] == 'malt' malt: it[2]['tool'] == 'malt'