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Debugging comment

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This commit is contained in:
James Fellows Yates 2022-03-28 09:13:05 +02:00
parent 8dc9e583ad
commit ee53283696
1 changed files with 5 additions and 1 deletions
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workflows/taxprofiler.nf
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@ -118,7 +118,6 @@ workflow TAXPROFILER {
/* /*
MODULE: PERFORM SHORT READ RUN MERGING MODULE: PERFORM SHORT READ RUN MERGING
*/
// Remove run accession to allow grouping by sample. Will only merge // Remove run accession to allow grouping by sample. Will only merge
// if pairment type is the same. // if pairment type is the same.
@ -128,6 +127,7 @@ workflow TAXPROFILER {
// e.g. `home jfellows Documents git nf-core taxprofiler testing work 68 9a2c8362add37832a776058d280bb7 2612_se.merged.fastq.gz` // e.g. `home jfellows Documents git nf-core taxprofiler testing work 68 9a2c8362add37832a776058d280bb7 2612_se.merged.fastq.gz`
// So theoretically need to force this into a list, (but results the can't access meta.id error as incorrect input format) // So theoretically need to force this into a list, (but results the can't access meta.id error as incorrect input format)
// But second issue >= 2 is MAYBE sufficient because what if merging two paired-end files? Need to chcek if the input channel formatted correctly for this? Need to check... // But second issue >= 2 is MAYBE sufficient because what if merging two paired-end files? Need to chcek if the input channel formatted correctly for this? Need to check...
ch_processed_for_combine = ch_shortreads_preprocessed ch_processed_for_combine = ch_shortreads_preprocessed
.dump(tag: "prep_for_combine_grouping") .dump(tag: "prep_for_combine_grouping")
.map { .map {
@ -160,6 +160,9 @@ workflow TAXPROFILER {
.dump(tag: "skip_combine") .dump(tag: "skip_combine")
.mix( CAT_FASTQ.out.reads ) .mix( CAT_FASTQ.out.reads )
.dump(tag: "files_for_profiling") .dump(tag: "files_for_profiling")
*/
ch_reads_for_profiling = ch_shortreads_preprocessed
/* /*
COMBINE READS WITH POSSIBLE DATABASES COMBINE READS WITH POSSIBLE DATABASES
@ -198,6 +201,7 @@ workflow TAXPROFILER {
} }
// We can run Kraken2 one-by-one sample-wise // We can run Kraken2 one-by-one sample-wise
// TODO Only flatten when paired-end! Causing issue commented out above!
ch_input_for_kraken2 = ch_input_for_profiling.kraken2 ch_input_for_kraken2 = ch_input_for_profiling.kraken2
.dump(tag: "input_to_kraken") .dump(tag: "input_to_kraken")
.multiMap { .multiMap {