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Debugging comment
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1 changed files with 5 additions and 1 deletions
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@ -118,7 +118,6 @@ workflow TAXPROFILER {
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/*
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MODULE: PERFORM SHORT READ RUN MERGING
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*/
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// Remove run accession to allow grouping by sample. Will only merge
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// if pairment type is the same.
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@ -128,6 +127,7 @@ workflow TAXPROFILER {
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// e.g. `home jfellows Documents git nf-core taxprofiler testing work 68 9a2c8362add37832a776058d280bb7 2612_se.merged.fastq.gz`
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// So theoretically need to force this into a list, (but results the can't access meta.id error as incorrect input format)
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// 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...
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ch_processed_for_combine = ch_shortreads_preprocessed
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.dump(tag: "prep_for_combine_grouping")
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.map {
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@ -160,6 +160,9 @@ workflow TAXPROFILER {
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.dump(tag: "skip_combine")
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.mix( CAT_FASTQ.out.reads )
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.dump(tag: "files_for_profiling")
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*/
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ch_reads_for_profiling = ch_shortreads_preprocessed
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/*
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COMBINE READS WITH POSSIBLE DATABASES
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@ -198,6 +201,7 @@ workflow TAXPROFILER {
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}
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// We can run Kraken2 one-by-one sample-wise
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// TODO Only flatten when paired-end! Causing issue commented out above!
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ch_input_for_kraken2 = ch_input_for_profiling.kraken2
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.dump(tag: "input_to_kraken")
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.multiMap {
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