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DSL1: Release 2.5.0 - Bopfingen #1032

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merged 32 commits into from
Nov 7, 2023
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870d2ca
Post patch release bump
jfy133 May 16, 2023
550225c
Add UDG info to trimbam output bam name.
TCLamnidis Aug 15, 2023
1005ce8
bump multiQC version
TCLamnidis Aug 15, 2023
09af474
add parameters to schema and config
TCLamnidis Aug 18, 2023
3d878c6
Add mapdamage as alternative damage estimator
TCLamnidis Aug 18, 2023
72854ee
rename parameter
TCLamnidis Aug 18, 2023
09ff881
Do not subsample by default in mapdamage
TCLamnidis Aug 18, 2023
eba08a2
Disable downsampling by default
TCLamnidis Aug 18, 2023
d794b8e
Add tests
TCLamnidis Aug 18, 2023
6aedb96
Update CHANGELOG.md
TCLamnidis Aug 18, 2023
1cae42d
Partial update to output.md
TCLamnidis Aug 18, 2023
7dc2334
pass mapdamage output to MQC
TCLamnidis Aug 22, 2023
b133d8b
Update output.md
TCLamnidis Aug 22, 2023
1d03083
Apply suggestions from code review
TCLamnidis Aug 23, 2023
8190c75
Standardise formatting of mapDamage across
TCLamnidis Aug 23, 2023
42d9dca
document besswarm plot fix
TCLamnidis Aug 30, 2023
3a84510
bump MultiQC version
TCLamnidis Oct 13, 2023
83163bb
mention NXF version cap. fix some broken URLs
TCLamnidis Oct 13, 2023
23b74e9
attempt to add mapadamage to multiqc
TCLamnidis Oct 13, 2023
322fdcd
tweak mqc mapdamage linking
TCLamnidis Oct 27, 2023
dabdee2
correct mqc version
TCLamnidis Oct 27, 2023
a61e83a
Update RG tags
TCLamnidis Oct 27, 2023
e87bad6
Update docs/output.md
TCLamnidis Oct 27, 2023
dd157ca
Merge branch 'patch' into dsl1-2.5.0
TCLamnidis Oct 27, 2023
92d8377
always index fasta if no fasta_index
TCLamnidis Nov 1, 2023
f0bd5be
Update Changelog
TCLamnidis Nov 1, 2023
754d5d8
add date to changelog
TCLamnidis Nov 1, 2023
b9c15ef
small bugfix
TCLamnidis Nov 1, 2023
e3b22ea
Merge pull request #1021 from nf-core/dsl1-2.5.0
TCLamnidis Nov 1, 2023
37d1482
bump versions
TCLamnidis Nov 1, 2023
5f2bffd
Apply suggestions from code review
TCLamnidis Nov 3, 2023
f3cde49
Update nextflow_schema.json
TCLamnidis Nov 3, 2023
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pass mapdamage output to MQC
  • Loading branch information
TCLamnidis committed Aug 22, 2023
commit 7dc233413f941b59726ba487b541157d88cd0fb8
2 changes: 2 additions & 0 deletions main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -2123,6 +2123,7 @@ process mapdamage_estimation {

output:
tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("results_*") into ch_output_from_mapdamage
path ("results_*") into ch_mapdamage_for_multiqc

script:
def base = "${bam.baseName}"
Expand Down Expand Up @@ -3257,6 +3258,7 @@ process multiqc {
file ('flagstat_filtered/*') from ch_bam_filtered_flagstat_for_multiqc.collect().ifEmpty([])
file ('preseq/*') from ch_preseq_for_multiqc.collect().ifEmpty([])
file ('damageprofiler/dmgprof*/*') from ch_damageprofiler_results.collect().ifEmpty([])
path ('mapdamage/*') from ch_mapdamage_for_multiqc.collect().ifEmpty([]).dump(tag:'ch_mapdamage_for_multiqc')
file ('qualimap/qualimap*/*') from ch_qualimap_results.collect().ifEmpty([])
file ('markdup/*') from ch_markdup_results_for_multiqc.collect().ifEmpty([])
file ('dedup*/*') from ch_dedup_results_for_multiqc.collect().ifEmpty([])
Expand Down