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run_malt false in test and add text in output.md

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sofstam 2023-02-17 15:38:36 +01:00
parent f0aa89cb87
commit 90a5668007
3 changed files with 4 additions and 3 deletions
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4
conf/test.config
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@ -25,7 +25,7 @@ params {
perform_shortread_qc = true perform_shortread_qc = true
perform_longread_qc = true perform_longread_qc = true
shortread_qc_mergepairs = true shortread_qc_mergepairs = true
perform_shortread_complexityfilter = false perform_shortread_complexityfilter = true
perform_shortread_hostremoval = true perform_shortread_hostremoval = true
perform_longread_hostremoval = true perform_longread_hostremoval = true
perform_runmerging = true perform_runmerging = true
@ -33,7 +33,7 @@ params {
run_kaiju = true run_kaiju = true
run_kraken2 = true run_kraken2 = true
run_bracken = true run_bracken = true
run_malt = true run_malt = false
run_metaphlan3 = true run_metaphlan3 = true
run_centrifuge = true run_centrifuge = true
run_diamond = true run_diamond = true

2
docs/output.md
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@ -463,6 +463,8 @@ The following report files are used for the taxpasta step:
- MetaPhlAn3: `<sample_id>_profile.txt` Taxpasta uses the `relative_abundance` column multiplied with a fixed number to yield an integer for the standardised profile. - MetaPhlAn3: `<sample_id>_profile.txt` Taxpasta uses the `relative_abundance` column multiplied with a fixed number to yield an integer for the standardised profile.
- mOTUs: `<sample_id>.out` Taxpasta uses the `read_count` column for the standardised profile. - mOTUs: `<sample_id>.out` Taxpasta uses the `read_count` column for the standardised profile.
Please aware the outputs of each tool's standardised profile _may not_ be directly comparable between each tool. Some may report raw read counts, whereas others may report abundance information. Please always refer to the list above, for which information is used for each tool.
### MultiQC ### MultiQC
<details markdown="1"> <details markdown="1">

1
subworkflows/local/standardisation_profiles.nf
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@ -141,7 +141,6 @@ workflow STANDARDISATION_PROFILES {
ch_multiqc_files = ch_multiqc_files.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.txt ) ch_multiqc_files = ch_multiqc_files.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.txt )
ch_versions = ch_versions.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.versions ) ch_versions = ch_versions.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.versions )
// mOTUs // mOTUs
// mOTUs has a 'single' database, and cannot create custom ones. // mOTUs has a 'single' database, and cannot create custom ones.