Change branch from master to main

pitagora-network · Mar 23, 2022 · c4dfeeb · c4dfeeb
1 parent 9e476f3
commit c4dfeeb
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Showing 8 changed files with 10 additions and 10 deletions.
diff --git a/test/tool/test_job/wget.yml b/test/tool/test_job/wget.yml
@@ -1,3 +1,3 @@
-use_remote_name: true  # type "boolean"
-url: https://raw.githubusercontent.com/pitagora-network/DAT2-cwl/master/README.md # type "string"
-track_location: false  # type "boolean"
+use_remote_name: true # type "boolean"
+url: https://raw.githubusercontent.com/pitagora-network/DAT2-cwl/main/README.md # type "string"
+track_location: false # type "boolean"
diff --git a/tool/for_trinity/build.sh b/tool/for_trinity/build.sh
@@ -2,5 +2,5 @@
 set -eux
 cd .
 
-wget https://raw.githubusercontent.com/bonohu/denovoTA/master/for_trinity.pl 
+wget https://raw.githubusercontent.com/bonohu/denovoTA/main/for_trinity.pl 
 docker build -t dat2-cwl/for_trinity .
diff --git a/tool/star/star_index/star_index.cwl b/tool/star/star_index/star_index.cwl
@@ -41,7 +41,7 @@ outputs:
       glob: $(inputs.genomeDir.basename)
 doc: >-
   STAR: Spliced Transcripts Alignment to a Reference.
-  https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf
+  https://github.com/alexdobin/STAR/blob/main/doc/STARmanual.pdf
 label: 'STAR genomeGenerate: Generating genome indexes.'
 requirements:
   - class: InitialWorkDirRequirement

diff --git a/tool/star/star_mapping-pe/star_mapping-pe.cwl b/tool/star/star_mapping-pe/star_mapping-pe.cwl
@@ -338,7 +338,7 @@ outputs:
         }
 doc: >-
   STAR: Spliced Transcripts Alignment to a Reference.
-  https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf
+  https://github.com/alexdobin/STAR/blob/main/doc/STARmanual.pdf
 label: 'STAR mapping: running mapping jobs.'
 requirements:
   - class: ShellCommandRequirement

diff --git a/tool/target2gene/build.sh b/tool/target2gene/build.sh
@@ -2,5 +2,5 @@
 set -eux
 cd .
 
-#wget https://raw.githubusercontent.com/bonohu/denovoTA/master/for_trinity.pl
+#wget https://raw.githubusercontent.com/bonohu/denovoTA/main/for_trinity.pl
 docker image build -t dat2-cwl/target2gene .
diff --git a/workflow/disease-genome/mapping-prepare-exome-data/mapping-prepare-exome-data.cwl b/workflow/disease-genome/mapping-prepare-exome-data/mapping-prepare-exome-data.cwl
@@ -17,7 +17,7 @@ steps:
     out:
       - downloaded
   sra2fastq:
-    run: https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/tools/fastq-dump/fastq-dump.cwl
+    run: https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/main/tools/fastq-dump/fastq-dump.cwl
     in:
       sraFiles:
         source: [download/downloaded]

diff --git a/workflow/epigenome-BS-seq/download_rawdata.cwl b/workflow/epigenome-BS-seq/download_rawdata.cwl
@@ -12,7 +12,7 @@ inputs:
     doc: "list of SRA Run ID e.g. SRR1274307"
 steps:
   download_fastq:
-    run: https://github.com/pitagora-network/pitagora-cwl/raw/master/workflows/download-fastq/download-fastq.cwl
+    run: https://github.com/pitagora-network/pitagora-cwl/raw/main/workflows/download-fastq/download-fastq.cwl
     in:
       run_ids: run_ids
     out:

diff --git a/workflow/epigenome-BS-seq/fastqc-workflow.cwl b/workflow/epigenome-BS-seq/fastqc-workflow.cwl
@@ -11,7 +11,7 @@ inputs:
     default: 4
 steps:
   fastqc:
-    run: https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/tools/fastqc/fastqc.cwl
+    run: https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/main/tools/fastqc/fastqc.cwl
     in:
       nogroup:
         default: true