Merge pull request #589 from FelixKrueger/dev

Pull in Docs changes
FelixKrueger · May 29, 2023 · 7288cb6 · 7288cb6
2 parents 1675a9c + 0530300
commit 7288cb6
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diff --git a/.github/workflows/ci_tests.yml b/.github/workflows/ci_tests.yml
@@ -13,7 +13,6 @@ jobs:
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
-
       - name: Check out Bismark source-code repository
         uses: actions/checkout@v2
 
@@ -44,85 +43,84 @@ jobs:
           samtools --version
           bowtie2 --version
           hisat2 --version
-        
+
       - name: Genome Preparation
         shell: bash -l {0} # required: yes! see above
         run: |
           pwd
-          ./bismark_genome_preparation --verbose ./travis_files/
-          ./bismark_genome_preparation --verbose --parallel 4 ./travis_files/
-          
+          ./bismark_genome_preparation --verbose ./test_files/
+          ./bismark_genome_preparation --verbose --parallel 4 ./test_files/
+
       - name: Bismark PE run
         shell: bash -l {0}
         run: |
-          ./bismark --genome ./travis_files/ -1 ./travis_files/test_R1.fastq.gz -2 ./travis_files/test_R2.fastq.gz
+          ./bismark --genome ./test_files/ -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
           ./deduplicate_bismark --bam test_R1_bismark_bt2_pe.bam
-          ./bismark_methylation_extractor test_R1_bismark_bt2_pe.bam --gzip --CX --bed --genome ./travis_files/
+          ./bismark_methylation_extractor test_R1_bismark_bt2_pe.bam --gzip --CX --bed --genome ./test_files/
           ./bismark2report
           ./bismark2summary
 
       - name: Bismark SE run
         shell: bash -l {0}
         run: |
-          ./bismark --genome ./travis_files/ ./travis_files/test_R1.fastq.gz
+          ./bismark --genome ./test_files/ ./test_files/test_R1.fastq.gz
           ./deduplicate_bismark --bam test_R1_bismark_bt2.bam
-          ./bismark_methylation_extractor test_R1_bismark_bt2.bam --gzip --CX --bed --genome ./travis_files/
-  
+          ./bismark_methylation_extractor test_R1_bismark_bt2.bam --gzip --CX --bed --genome ./test_files/
+
       - name: Bismark run with option ICPC
         shell: bash -l {0}
         run: |
-          ./bismark --bowtie2 --icpc ./travis_files/ -1 ./travis_files/test_R1.fastq.gz -2 ./travis_files/test_R2.fastq.gz
-          ./bismark --bowtie2 --icpc ./travis_files/ ./travis_files/test_R1.fastq.gz
+          ./bismark --bowtie2 --icpc ./test_files/ -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
+          ./bismark --bowtie2 --icpc ./test_files/ ./test_files/test_R1.fastq.gz
 
       - name: Bismark run using HISAT2
         shell: bash -l {0}
         run: |
-          ./bismark_genome_preparation --hisat2 --verbose ./travis_files/
-          ./bismark_genome_preparation --hisat2 --verbose --parallel 4 ./travis_files/
-          ./bismark --genome ./travis_files/ --hisat2 ./travis_files/test_R1.fastq.gz
-          ./bismark --genome ./travis_files/ --hisat2 -1 ./travis_files/test_R1.fastq.gz -2 ./travis_files/test_R2.fastq.gz
+          ./bismark_genome_preparation --hisat2 --verbose ./test_files/
+          ./bismark_genome_preparation --hisat2 --verbose --parallel 4 ./test_files/
+          ./bismark --genome ./test_files/ --hisat2 ./test_files/test_R1.fastq.gz
+          ./bismark --genome ./test_files/ --hisat2 -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
           ./deduplicate_bismark --bam test_R1_bismark_hisat2.bam
-          ./bismark_methylation_extractor test_R1_bismark_hisat2.bam  --gzip --CX --bed --genome ./travis_files/
-          ./bismark_methylation_extractor test_R1_bismark_hisat2_pe.bam  --gzip --CX --bed --genome ./travis_files/
-  
+          ./bismark_methylation_extractor test_R1_bismark_hisat2.bam  --gzip --CX --bed --genome ./test_files/
+          ./bismark_methylation_extractor test_R1_bismark_hisat2_pe.bam  --gzip --CX --bed --genome ./test_files/
+
       - name: Bismark run Multicore
         shell: bash -l {0}
         run: |
-          ./bismark --genome ./travis_files/ --parallel 4 -1 ./travis_files/test_R1.fastq.gz -2 ./travis_files/test_R2.fastq.gz
-          ./bismark --genome ./travis_files/ --hisat2 --parallel 4 -1 ./travis_files/test_R1.fastq.gz -2 ./travis_files/test_R2.fastq.gz         
-          ./bismark_methylation_extractor test_R1_bismark_bt2_pe.bam --gzip --CX --bed --parallel 8 --genome ./travis_files/
-          ./bismark_methylation_extractor test_R1_bismark_hisat2_pe.bam --gzip --CX --bed --parallel 8 --genome ./travis_files/
-      
+          ./bismark --genome ./test_files/ --parallel 4 -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
+          ./bismark --genome ./test_files/ --hisat2 --parallel 4 -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
+          ./bismark_methylation_extractor test_R1_bismark_bt2_pe.bam --gzip --CX --bed --parallel 8 --genome ./test_files/
+          ./bismark_methylation_extractor test_R1_bismark_hisat2_pe.bam --gzip --CX --bed --parallel 8 --genome ./test_files/
+
       - name: coverage2cytosine
         shell: bash -l {0}
         run: |
-          ./coverage2cytosine test_R1_bismark_bt2_pe.bismark.cov.gz --merge_CpG --genome ./travis_files/ -o test.output
-          ./coverage2cytosine test_R1_bismark_bt2_pe.bismark.cov.gz --NOMe-seq --genome ./travis_files/ -o test.output
-    
+          ./coverage2cytosine test_R1_bismark_bt2_pe.bismark.cov.gz --merge_CpG --genome ./test_files/ -o test.output
+          ./coverage2cytosine test_R1_bismark_bt2_pe.bismark.cov.gz --NOMe-seq --genome ./test_files/ -o test.output
+
       - name: bam2nuc
         shell: bash -l {0}
         run: |
-          ./bam2nuc --genome_folder ./travis_files/ --genomic_composition_only
-          ./bam2nuc --genome_folder ./travis_files/ test_R1_bismark_bt2_pe.bam
-          ./bam2nuc --genome_folder ./travis_files/ test_R1_bismark_hisat2_pe.bam
-  
+          ./bam2nuc --genome_folder ./test_files/ --genomic_composition_only
+          ./bam2nuc --genome_folder ./test_files/ test_R1_bismark_bt2_pe.bam
+          ./bam2nuc --genome_folder ./test_files/ test_R1_bismark_hisat2_pe.bam
+
       - name: Additional scenarios
         shell: bash -l {0}
         run: |
-          ./bismark --pbat --genome ./travis_files/ -1 ./travis_files/test_R1.fastq.gz -2 ./travis_files/test_R2.fastq.gz
-          ./bismark --non_directional --genome ./travis_files/ -1 ./travis_files/test_R1.fastq.gz -2 ./travis_files/test_R2.fastq.gz
-          ./bismark --hisat2 --pbat --genome ./travis_files/ -1 ./travis_files/test_R1.fastq.gz -2 ./travis_files/test_R2.fastq.gz
-          ./bismark --hisat2 --non_directional --genome ./travis_files/ -1 ./travis_files/test_R1.fastq.gz -2 ./travis_files/test_R2.fastq.gz
-        
-   
+          ./bismark --pbat --genome ./test_files/ -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
+          ./bismark --non_directional --genome ./test_files/ -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
+          ./bismark --hisat2 --pbat --genome ./test_files/ -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
+          ./bismark --hisat2 --non_directional --genome ./test_files/ -1 ./test_files/test_R1.fastq.gz -2 ./test_files/test_R2.fastq.gz
+
       - name: bismark2bedGraph
         shell: bash -l {0}
         run: |
           ./bismark2bedGraph -o test.bedGraph --buffer 5G CpG_*
           ./bismark2bedGraph -o test.bedGraph --ucsc --buffer 5G CpG_*
           ./bismark2bedGraph -o test.bedGraph --CX --scaffolds CpG* CHG_* CHH_*
           ./bismark2bedGraph -o test.bedGraph --CX --ample_memory --zero_based CpG* CHH_* CHG_*
-  
+
       - name: Filte non-conversion
         shell: bash -l {0}
         run: |

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -0,0 +1,20 @@
+name: ci
+on:
+  push:
+    branches:
+      - master
+      - dev
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.x
+      - uses: actions/cache@v2
+        with:
+          key: ${{ github.ref }}
+          path: .cache
+      - run: pip install mkdocs-material pillow cairosvg
+      - run: mkdocs gh-deploy --force
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1 @@
+.cache
diff --git a/.prettierignore b/.prettierignore
@@ -0,0 +1,2 @@
+docs/images/bismark_summary_report.html
+plotly/
diff --git a/.prettierrc.yaml b/.prettierrc.yaml
@@ -0,0 +1 @@
+tabWidth: 2