kids-first / kf-rnaseq-workflow Goto Github PK

There are a couple of tools where the IDs clash, for example:

arriba_draw_fusion.cwl and arriba_fusion.cwl

kallisto_calc_expression.cwl and kallisto_calc_expression_with_fusion.cwl

Suggested fix:

diff --git a/tools/arriba_draw_fusion.cwl b/tools/arriba_draw_fusion.cwl
index faf1dcf..39d6da1 100644
--- a/tools/arriba_draw_fusion.cwl
+++ b/tools/arriba_draw_fusion.cwl
@@ -1,6 +1,6 @@
 cwlVersion: v1.0
 class: CommandLineTool
-id: arriba_fusion
+id: arriba_draw_fusion
 requirements:
   - class: ShellCommandRequirement
   - class: DockerRequirement
diff --git a/tools/kallisto_calc_expression_with_fusion.cwl b/tools/kallisto_calc_expression_with_fusion.cwl
index b6860ed..a7ccf72 100644
--- a/tools/kallisto_calc_expression_with_fusion.cwl
+++ b/tools/kallisto_calc_expression_with_fusion.cwl
@@ -1,6 +1,6 @@
 cwlVersion: v1.0
 class: CommandLineTool
-id: kallisto
+id: kallisto_with_fusion
 requirements:
   - class: ShellCommandRequirement
   - class: DockerRequirement

@migbro should you hard code STAR version here? https://github.com/kids-first/kf-rnaseq-workflow/blob/master/tools/star_align.cwl

I did not check all, but specifically, this wf does not have links to the reference files, except for the fusion reference.

Please use this: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03922-7

Hi, we are trying to use your pipeline and encountered a problem while trying to download GRCh38_v27_CTAT_lib_Feb092018.plug-n-play.tar.gz from broad. This file is no longer available (they provide only source data for this genecode version: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.3/). Would you recommend to upgrade the genecode version for all input data? Or maybe you could provide a copy of GRCh38_v27_CTAT_lib_Feb092018.plug-n-play.tar.gz file if it is still available on your server?
Thanks!