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Re-add run merging and gonna let GHA see if it works >.>

This commit is contained in:
James Fellows Yates 2022-04-08 11:54:54 +02:00
parent 4c4475c316
commit 7b08c49cd6
3 changed files with 26 additions and 2 deletions

View file

@ -39,6 +39,7 @@ jobs:
- "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs" - "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs"
- "--shortread_complexityfilter_tool bbduk" - "--shortread_complexityfilter_tool bbduk"
- "--shortread_complexityfilter_tool prinseq" - "--shortread_complexityfilter_tool prinseq"
- "--run_merging"
steps: steps:
- name: Check out pipeline code - name: Check out pipeline code

View file

@ -76,6 +76,8 @@ params {
shortread_complexityfilter_prinseqplusplus_dustscore = 0.5 shortread_complexityfilter_prinseqplusplus_dustscore = 0.5
save_complexityfiltered_reads = false save_complexityfiltered_reads = false
// run merging
run_merging = false
// MALT // MALT
run_malt = false run_malt = false

View file

@ -125,13 +125,34 @@ workflow TAXPROFILER {
ch_shortreads_filtered = ch_shortreads_preprocessed ch_shortreads_filtered = ch_shortreads_preprocessed
} }
/*
STEP: Run merging
*/
if ( params.run_merging ) {
ch_reads_for_cat = ch_shortreads_filtered
.mix( ch_longreads_preprocessed )
.map {
meta, reads ->
def meta_new = meta.clone()
meta_new['run_accession'].remove()
[ meta_new, reads ]
}
.groupTuple()
ch_reads_runmerged = CAT_FASTQ ( ch_reads_for_cat )
} else {
ch_reads_runmerged = ch_shortreads_filtered
.mix( ch_longreads_preprocessed )
}
/* /*
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_shortreads_filtered ch_input_for_profiling = ch_reads_runmerged
.mix( ch_longreads_preprocessed )
.combine(DB_CHECK.out.dbs) .combine(DB_CHECK.out.dbs)
.branch { .branch {
malt: it[2]['tool'] == 'malt' malt: it[2]['tool'] == 'malt'