mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-14 17:33:09 +00:00
Re-add run merging and gonna let GHA see if it works >.>
This commit is contained in:
parent
4c4475c316
commit
7b08c49cd6
3 changed files with 26 additions and 2 deletions
1
.github/workflows/ci.yml
vendored
1
.github/workflows/ci.yml
vendored
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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'
|
||||||
|
|
Loading…
Reference in a new issue