From fd19cd31c0749c949e1ffd51c45b153780fe0d10 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 19 Dec 2018 13:25:36 +0100 Subject: [PATCH 1/2] Add functionality to work with DamageProfiler in Multiqc 1.7dev and higher --- environment.yml | 2 +- main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/environment.yml b/environment.yml index 520e4c206..e2d909448 100644 --- a/environment.yml +++ b/environment.yml @@ -17,7 +17,7 @@ dependencies: - bioconda::gatk4=4.0.11.0 - bioconda::qualimap=2.2.2b - bioconda::vcf2genome=0.91 - - bioconda::damageprofiler=0.3.11 + - bioconda::damageprofiler=0.4.2 - bioconda::multiqc=1.6 - bioconda::pmdtools=0.60 - conda-forge::r-rmarkdown=1.10 diff --git a/main.nf b/main.nf index 868b1424d..1a8f44d9e 100644 --- a/main.nf +++ b/main.nf @@ -870,7 +870,7 @@ process damageprofiler { file fasta from ch_fasta_for_damageprofiler output: - file "*" into ch_damageprofiler_results + file "*.yaml" into ch_damageprofiler_results script: """ From 04d6be2edd9c5b2d404a0b6a13c29991f7bd6565 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Sat, 22 Dec 2018 15:15:36 +0100 Subject: [PATCH 2/2] MQC 1.7 and DamageProfiler supported now in EAGER --- environment.yml | 4 ++-- main.nf | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/environment.yml b/environment.yml index e2d909448..56ac833a2 100644 --- a/environment.yml +++ b/environment.yml @@ -17,8 +17,8 @@ dependencies: - bioconda::gatk4=4.0.11.0 - bioconda::qualimap=2.2.2b - bioconda::vcf2genome=0.91 - - bioconda::damageprofiler=0.4.2 - - bioconda::multiqc=1.6 + - bioconda::damageprofiler=0.4.4 + - bioconda::multiqc=1.7 - bioconda::pmdtools=0.60 - conda-forge::r-rmarkdown=1.10 - conda-forge::libiconv=1.15 diff --git a/main.nf b/main.nf index 1a8f44d9e..9115d8e10 100644 --- a/main.nf +++ b/main.nf @@ -870,7 +870,7 @@ process damageprofiler { file fasta from ch_fasta_for_damageprofiler output: - file "*.yaml" into ch_damageprofiler_results + file "*.json" into ch_damageprofiler_results script: """