From ee53283696261fa2687fa55402e3cfa3da164509 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Mon, 28 Mar 2022 09:13:05 +0200 Subject: [PATCH] Debugging comment --- workflows/taxprofiler.nf | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/workflows/taxprofiler.nf b/workflows/taxprofiler.nf index 87f7a30..8a05720 100644 --- a/workflows/taxprofiler.nf +++ b/workflows/taxprofiler.nf @@ -118,7 +118,6 @@ workflow TAXPROFILER { /* MODULE: PERFORM SHORT READ RUN MERGING - */ // Remove run accession to allow grouping by sample. Will only merge // 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` // 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... + ch_processed_for_combine = ch_shortreads_preprocessed .dump(tag: "prep_for_combine_grouping") .map { @@ -160,6 +160,9 @@ workflow TAXPROFILER { .dump(tag: "skip_combine") .mix( CAT_FASTQ.out.reads ) .dump(tag: "files_for_profiling") + */ + + ch_reads_for_profiling = ch_shortreads_preprocessed /* COMBINE READS WITH POSSIBLE DATABASES @@ -198,6 +201,7 @@ workflow TAXPROFILER { } // 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 .dump(tag: "input_to_kraken") .multiMap {