Change branch from develop to main

README.md

@@ -2,8 +2,6 @@
 
 This repository contains the Common Workflow Language (CWL) definitions of the workflows introduced in the book [#NGS_DAT 2nd edition (A tutorial book in Japanese, 次世代シークエンサー DRY 解析教本 改訂第 2 版)](https://www.amazon.co.jp/dp/478090983X).
 
-Go to [`develop`](https://github.com/pitagora-network/DAT2-cwl/tree/develop) branch to test the workflows in development.
-
 ## Workflows
 
 - animal-genome-assembly by [inutano](https://github.com/inutano)
@@ -67,7 +65,7 @@ All workflows introduced in the book has been translated in CWL, but yet the tes
 p.333 に記載のある URL `https://tinyurl.com/dat2_cwl_example` がアクセス不能となっています。すみません。こちらで指定すべきコマンドと URL はこちらです。(コピペする場合は `$` は除いてください)
 
 ```
-$ cwltool https://raw.githubusercontent.com/pitagora-network/DAT2-cwl/develop/workflow/meta16s-seq/meta16s-seq.demo.cwl
+$ cwltool https://raw.githubusercontent.com/pitagora-network/DAT2-cwl/main/workflow/meta16s-seq/meta16s-seq.demo.cwl
 ```
 
 ## Troubleshooting
@@ -76,4 +74,4 @@ Please create an issue on [github issue](https://github.com/pitagora-network/DAT
 
 ## Copyright
 
-Copyright (c) 2020 [Contributors](https://github.com/pitagora-network/DAT2-cwl/graphs/contributors). See [LICENSE](https://raw.githubusercontent.com/pitagora-network/DAT2-cwl/develop/LICENSE) for further details.
+Copyright (c) 2020 [Contributors](https://github.com/pitagora-network/DAT2-cwl/graphs/contributors). See [LICENSE](https://raw.githubusercontent.com/pitagora-network/DAT2-cwl/main/LICENSE) for further details.

workflow/epigenome-BS-seq/bismark_genome_preparation_workflow.cwl

@@ -30,7 +30,7 @@ steps:
     out: [ renamed_dir ]
 
   bismark_genome_preparation:
-    run: https://raw.githubusercontent.com/pitagora-network/DAT2-cwl/develop/tool/bismark/bismark_genome_preparation/bismark_genome_preparation.cwl
+    run: https://raw.githubusercontent.com/pitagora-network/DAT2-cwl/main/tool/bismark/bismark_genome_preparation/bismark_genome_preparation.cwl
     in:
       ref_directory: rename/renamed_dir
     out:

workflow/epigenome-BS-seq/download_rawdata.cwl

@@ -18,7 +18,7 @@ steps:
     out:
       [fastq_files]
   gunzip:
-    run: https://raw.githubusercontent.com/pitagora-network/DAT2-cwl/develop/tool/gunzip/gunzip.cwl
+    run: https://raw.githubusercontent.com/pitagora-network/DAT2-cwl/main/tool/gunzip/gunzip.cwl
     in:
       file: download_fastq/fastq_files
     scatter: file

workflow/epigenome-BS-seq/download_reference_fasta.cwl

@@ -15,15 +15,15 @@ inputs:
 
 steps:
   wget:
-    run: https://raw.githubusercontent.com/pitagora-network/DAT2-cwl/develop/tool/wget/wget.cwl
+    run: https://raw.githubusercontent.com/pitagora-network/DAT2-cwl/main/tool/wget/wget.cwl
     in:
       url: url
       use_remote_name:
         default: true
     out:
       [downloaded]
   tar:
-    run: https://raw.githubusercontent.com/pitagora-network/DAT2-cwl/develop/tool/tar/tar.cwl
+    run: https://raw.githubusercontent.com/pitagora-network/DAT2-cwl/main/tool/tar/tar.cwl
     in:
       file: wget/downloaded
       extract:
@@ -33,7 +33,7 @@ steps:
     out:
       [output]
   lists:
-    run: https://raw.githubusercontent.com/pitagora-network/DAT2-cwl/develop/tool/listing/listing.cwl
+    run: https://raw.githubusercontent.com/pitagora-network/DAT2-cwl/main/tool/listing/listing.cwl
     in:
       dir: tar/output
       file_names:
@@ -67,7 +67,7 @@ steps:
     out:
       [files]
   cat:
-    run: https://raw.githubusercontent.com/pitagora-network/DAT2-cwl/develop/tool/cat/cat.cwl
+    run: https://raw.githubusercontent.com/pitagora-network/DAT2-cwl/main/tool/cat/cat.cwl
     in:
       files: lists/files
     out:

workflow/epigenome-BS-seq/epigenome-BS-seq.cwl

@@ -42,7 +42,7 @@ steps:
       fastq_files: download_rawdata/fastq_files
     out: [output]
   trim_galore_rawdata:
-    run: https://raw.githubusercontent.com/pitagora-network/DAT2-cwl/develop/tool/trim_galore/trim_galore.cwl
+    run: https://raw.githubusercontent.com/pitagora-network/DAT2-cwl/main/tool/trim_galore/trim_galore.cwl
     in:
       nogroup:
         default: true
@@ -63,7 +63,7 @@ steps:
     out:
       - output
   bismark_exec:
-    run: https://raw.githubusercontent.com/pitagora-network/DAT2-cwl/develop/tool/bismark/bismark/bismark.cwl
+    run: https://raw.githubusercontent.com/pitagora-network/DAT2-cwl/main/tool/bismark/bismark/bismark.cwl
     in:
       genome_folder: bismark_genome_preparation/output
       fq: trim_galore_rawdata/fq