From 70eb84b8d5d310c666d0de2fb5f9db401571cc39 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 9 Feb 2023 08:01:52 +0100 Subject: [PATCH] Apply suggestions from code review Co-authored-by: Moritz E. Beber --- conf/modules.config | 1 + docs/usage.md | 2 +- subworkflows/local/profiling.nf | 3 --- 3 files changed, 2 insertions(+), 4 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 47c4663..b0a6e03 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -359,6 +359,7 @@ process { } withName: BRACKEN_BRACKEN { + errorStrategy = 'ignore' ext.args = { "${meta.db_params}" } ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.bracken" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.bracken" } publishDir = [ diff --git a/docs/usage.md b/docs/usage.md index 53dc8c3..523d92a 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -103,7 +103,7 @@ metaphlan3,db1,,///metaphlan3/metaphlan_database/ motus,db_mOTU,,///motus/motus_database/ ``` -For Bracken, if you wish to supply amy parameters to either the Kraken or Bracken step you **must** have a _semi-colon_ `;` list as in `db_params`. This is to allow to specify the Kraken2 parameters before, and Bracken parameters after the `;` as Bracken is a two step process. This is particularly important if you supply a Bracken database with a non-default read length parameter. If you do not have any parameters to specify, you can leave this as empty. +For Bracken, if you wish to supply any parameters to either the Kraken or Bracken step you **must** have a _semi-colon_ `;` list as in `db_params`. This is to allow to specify the Kraken2 parameters before, and Bracken parameters after the `;` as Bracken is a two step process. This is particularly important if you supply a Bracken database with a non-default read length parameter. If you do not have any parameters to specify, you can leave this as empty. Column specifications are as follows: diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf index 16caa8f..cf5a9b8 100644 --- a/subworkflows/local/profiling.nf +++ b/subworkflows/local/profiling.nf @@ -141,7 +141,6 @@ workflow PROFILING { [ meta, reads, db_meta_new, db ] } - .dump(tag: "ch_input_for_kraken2_after") .multiMap { it -> reads: [ it[0] + it[2], it[1] ] @@ -184,7 +183,6 @@ workflow PROFILING { ch_input_for_bracken = ch_kraken2_output .map { meta, report -> [meta['db_name'], meta, report] } .combine(ch_bracken_databases, by: 0) - .dump(tag: "ch_input_for_bracken_b4") .map { key, meta, reads, db_meta, db -> @@ -208,7 +206,6 @@ workflow PROFILING { [ key, meta, reads, db_meta_new, db ] } - .dump(tag: "ch_input_for_bracken_after") .multiMap { key, meta, report, db_meta, db -> report: [meta + db_meta, report] db: db