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Re-add run merging and gonna let GHA see if it works >.>
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3 changed files with 26 additions and 2 deletions
1
.github/workflows/ci.yml
vendored
1
.github/workflows/ci.yml
vendored
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@ -39,6 +39,7 @@ jobs:
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- "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs"
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- "--shortread_complexityfilter_tool bbduk"
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- "--shortread_complexityfilter_tool prinseq"
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- "--run_merging"
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steps:
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- name: Check out pipeline code
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@ -76,6 +76,8 @@ params {
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shortread_complexityfilter_prinseqplusplus_dustscore = 0.5
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save_complexityfiltered_reads = false
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// run merging
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run_merging = false
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// MALT
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run_malt = false
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@ -125,13 +125,34 @@ workflow TAXPROFILER {
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ch_shortreads_filtered = ch_shortreads_preprocessed
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}
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/*
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STEP: Run merging
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*/
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if ( params.run_merging ) {
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ch_reads_for_cat = ch_shortreads_filtered
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.mix( ch_longreads_preprocessed )
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.map {
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meta, reads ->
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def meta_new = meta.clone()
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meta_new['run_accession'].remove()
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[ meta_new, reads ]
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}
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.groupTuple()
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ch_reads_runmerged = CAT_FASTQ ( ch_reads_for_cat )
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} else {
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ch_reads_runmerged = ch_shortreads_filtered
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.mix( ch_longreads_preprocessed )
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}
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/*
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COMBINE READS WITH POSSIBLE DATABASES
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*/
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// 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]
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ch_input_for_profiling = ch_shortreads_filtered
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.mix( ch_longreads_preprocessed )
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ch_input_for_profiling = ch_reads_runmerged
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.combine(DB_CHECK.out.dbs)
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.branch {
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malt: it[2]['tool'] == 'malt'
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