From c53b2360599c2d7981fce93925d409409d1d5a7b Mon Sep 17 00:00:00 2001 From: David JM Date: Thu, 26 Oct 2023 15:35:43 -0700 Subject: [PATCH 1/4] chore: update gitignore --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index 5a84666..75377b3 100644 --- a/.gitignore +++ b/.gitignore @@ -16,3 +16,4 @@ pyenv372 .python-version .Rproj.user scripts/scripts.Rproj +scripts/.Rhistory From be7023fe6ab2b4c99f09fb5f12342287c7f24c5b Mon Sep 17 00:00:00 2001 From: David JM Date: Thu, 26 Oct 2023 15:36:12 -0700 Subject: [PATCH 2/4] update: new plexedpiper version 0.4.2 --- dockerfiles/Dockerfile.plexedpiper | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dockerfiles/Dockerfile.plexedpiper b/dockerfiles/Dockerfile.plexedpiper index fb1ece2..fad195b 100644 --- a/dockerfiles/Dockerfile.plexedpiper +++ b/dockerfiles/Dockerfile.plexedpiper @@ -13,6 +13,6 @@ RUN apt-get update \ # hadolint ignore=DL3059 RUN R -e 'install.packages("devtools")' \ - && R -e 'remotes::install_github("PNNL-Comp-Mass-Spec/PlexedPiper@0.4.1", build_vignettes = FALSE)' \ + && R -e 'remotes::install_github("PNNL-Comp-Mass-Spec/PlexedPiper@0.4.2", build_vignettes = FALSE)' \ && R -e 'install.packages("optparse")' \ && R -e 'install.packages("purrr")' From 27c0460ae1331019354c90a2e0b46b28c72b6170 Mon Sep 17 00:00:00 2001 From: David JM Date: Thu, 26 Oct 2023 15:37:01 -0700 Subject: [PATCH 3/4] update: add pipeline output to msgfplus pipeline --- wdl/proteomics_msgfplus.wdl | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/wdl/proteomics_msgfplus.wdl b/wdl/proteomics_msgfplus.wdl index 2ecd654..2f65598 100644 --- a/wdl/proteomics_msgfplus.wdl +++ b/wdl/proteomics_msgfplus.wdl @@ -267,6 +267,11 @@ workflow proteomics_msgfplus { isPTM = isPTM } } + + output { + File? results_rii = wrapper_pp.results_rii + File? results_ratio = wrapper_pp.results_ratio + } } task msgf_sequences { From 58374ef1a616be25b0e753fc3807738cc592adcd Mon Sep 17 00:00:00 2001 From: David JM Date: Thu, 26 Oct 2023 15:52:05 -0700 Subject: [PATCH 4/4] bump version 1.0.1 --- wdl/proteomics_msgfplus.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wdl/proteomics_msgfplus.wdl b/wdl/proteomics_msgfplus.wdl index 2f65598..b841850 100644 --- a/wdl/proteomics_msgfplus.wdl +++ b/wdl/proteomics_msgfplus.wdl @@ -3,7 +3,7 @@ version 1.0 workflow proteomics_msgfplus { meta { author: "David Jimenez-Morales" - version: "v1.0.0" + version: "v1.0.1" task_labels: { msgf_sequences: {