Merge pull request #140 from CCBR/prettier

style: run prettier on all files

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,20 +1,21 @@
 ---
 name: Bug report
 about: Create a report to help us improve
-title: ''
-labels: ''
-assignees: 'slsevilla'
+title: ""
+labels: ""
+assignees: "slsevilla"
 ---
 
 **Describe the bug**
 A clear and concise description of what the bug is.
 
 **To Reproduce**
 Steps to reproduce the behavior; if applicable, add screenshots to help explain your problem:
+
 1. Go to '...'
 2. Click on '....'
 3. Scroll down to '....'
 4. See error
 
 **Expected behavior**
-A clear and concise description of what you expected to happen.
+A clear and concise description of what you expected to happen.

.github/ISSUE_TEMPLATE/enchancement_request.md

@@ -1,14 +1,13 @@
 ---
 name: Enhancement request
 about: Suggest an additional component to an already existing feature
-title: ''
-labels: ''
-assignees: 'slsevilla'
-
+title: ""
+labels: ""
+assignees: "slsevilla"
 ---
 
 **Describe what enhancement you'd like to see.**
 A clear and concise description of what you'd like to add, specifically to what already existing feature. Ex. I am using a new reference, and I'd love to see this reference included [...]
 
 **Additional context**
-Add any other context or screenshots about the feature request here.
+Add any other context or screenshots about the feature request here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,13 +1,13 @@
 ---
 name: Feature request
 about: Suggest an idea for this project
-title: ''
-labels: ''
-assignees: 'slsevilla'
+title: ""
+labels: ""
+assignees: "slsevilla"
 ---
 
 **Is your feature request related to a problem? Please describe.**
 A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
 
 **Describe the solution you'd like**
-A clear and concise description of what you want to happen. If there are alternative solutions or features you've considered, please include these!
+A clear and concise description of what you want to happen. If there are alternative solutions or features you've considered, please include these!

.github/workflows/build_mkdocs.yaml

@@ -3,7 +3,7 @@ on:
   workflow_dispatch:
   push:
     paths:
-      - 'docs/**'
+      - "docs/**"
 jobs:
   deploy:
     runs-on: ubuntu-latest
@@ -14,4 +14,4 @@ jobs:
           python-version: 3.9
       - run: pip install --upgrade pip
       - run: pip install -r docs/requirements.txt
-      - run: mkdocs gh-deploy --force
+      - run: mkdocs gh-deploy --force

.github/workflows/lintr.yaml

@@ -13,18 +13,18 @@ jobs:
   Lintr:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-    - uses: docker://snakemake/snakemake:v7.19.1
-    - name: Lint Workflow
-      continue-on-error: true
-      run: |
-        docker run -v $PWD:/opt2 snakemake/snakemake:v7.19.1 /bin/bash -c \
-        "mkdir -p /opt2/output_carlisle/config /opt2/output_carlisle/annotation && \
-        cp -r /opt2/workflow/scripts/ /opt2/output_carlisle/ && \
-        cp /opt2/resources/cluster_biowulf.yaml /opt2/output_carlisle/config/cluster.yaml && \
-        cp /opt2/resources/tools_biowulf.yaml /opt2/output_carlisle/config/tools.yaml && \
-        cd /opt2/output_carlisle/annotation && \
-        touch hg38.fa genes.gtf hg38.bed hg38.tss.bed hg38_refseq.ucsc Ecoli_GCF_000005845.2_ASM584v2_genomic.fna adapters.fa && \
-        snakemake --lint -s /opt2/workflow/Snakefile \
-        -d /opt2/output_carlisle --configfile /opt2/.test/config_lint.yaml || \
-        echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.'"
+      - uses: actions/checkout@v2
+      - uses: docker://snakemake/snakemake:v7.19.1
+      - name: Lint Workflow
+        continue-on-error: true
+        run: |
+          docker run -v $PWD:/opt2 snakemake/snakemake:v7.19.1 /bin/bash -c \
+          "mkdir -p /opt2/output_carlisle/config /opt2/output_carlisle/annotation && \
+          cp -r /opt2/workflow/scripts/ /opt2/output_carlisle/ && \
+          cp /opt2/resources/cluster_biowulf.yaml /opt2/output_carlisle/config/cluster.yaml && \
+          cp /opt2/resources/tools_biowulf.yaml /opt2/output_carlisle/config/tools.yaml && \
+          cd /opt2/output_carlisle/annotation && \
+          touch hg38.fa genes.gtf hg38.bed hg38.tss.bed hg38_refseq.ucsc Ecoli_GCF_000005845.2_ASM584v2_genomic.fna adapters.fa && \
+          snakemake --lint -s /opt2/workflow/Snakefile \
+          -d /opt2/output_carlisle --configfile /opt2/.test/config_lint.yaml || \
+          echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.'"

.github/workflows/test_dev.yml

@@ -13,20 +13,20 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/[email protected]
-    - uses: docker://snakemake/snakemake:v7.19.1
-      with:
-        directory: '.test'
-    - name: dryrun
-      shell: bash {0}
-      run: |
-        bash ./install.sh ./test-workdir/carlisle-v9999.9999.9999-dev
-        ./test-workdir/carlisle-v9999.9999.9999-dev/bin/carlisle --runmode=init --workdir=./test-workdir/output_carlisle
-        cp ./test-workdir/carlisle-v9999.9999.9999-dev/bin/.test/config_lint.yaml ./test-workdir/output_carlisle/config/config.yaml
-        # TODO: use `carlisle run --mode dryrun`
-        docker run -v ./test-workdir/:/opt2 snakemake/snakemake:v7.19.1 /bin/bash -c \
-          "cd /opt2 && snakemake \
-            -s ./carlisle-v9999.9999.9999-dev/bin/workflow/Snakefile \
-            --dryrun \
-            --configfile carlisle-v9999.9999.9999-dev/bin/.test/config_lint.yaml \
-            --directory output_carlisle"
+      - uses: actions/[email protected]
+      - uses: docker://snakemake/snakemake:v7.19.1
+        with:
+          directory: ".test"
+      - name: dryrun
+        shell: bash {0}
+        run: |
+          bash ./install.sh ./test-workdir/carlisle-v9999.9999.9999-dev
+          ./test-workdir/carlisle-v9999.9999.9999-dev/bin/carlisle --runmode=init --workdir=./test-workdir/output_carlisle
+          cp ./test-workdir/carlisle-v9999.9999.9999-dev/bin/.test/config_lint.yaml ./test-workdir/output_carlisle/config/config.yaml
+          # TODO: use `carlisle run --mode dryrun`
+          docker run -v ./test-workdir/:/opt2 snakemake/snakemake:v7.19.1 /bin/bash -c \
+            "cd /opt2 && snakemake \
+              -s ./carlisle-v9999.9999.9999-dev/bin/workflow/Snakefile \
+              --dryrun \
+              --configfile carlisle-v9999.9999.9999-dev/bin/.test/config_lint.yaml \
+              --directory output_carlisle"

.test/README.md

@@ -1,6 +1,9 @@
 ################################################
+
 # CHANGELOG
+
 ### samples retired 2/6/24
+
 <!-- VS589.R1.fastq.gz,HN6_H3K4me3_2.R1.fastq.gz
 VS589.R2.fastq.gz,HN6_H3K4me3_2.R2.fastq.gz
 VS594.R1.fastq.gz,HN6_H4K20me3_1.R1.fastq.gz
@@ -10,15 +13,21 @@ VS595.R2.fastq.gz,HN6_H4K20me3_2.R2.fastq.gz
 VS597.R1.fastq.gz,53_H4K20m3_1.R1.fastq.gz
 VS597.R2.fastq.gz,53_H4K20m3_1.R2.fastq.gz
 VS598.R1.fastq.gz,53_H4K20m3_2.R1.fastq.gz -->
+
 ### 12/16/22
+
 New test data is added to pipeline
 
 ################################################
+
 # HG38
+
 # sample location
+
 /data/CCBR/projects/ccbr1155/CS031014/fastq
 
 # sample ids mapping; original to renamed
+
 VS586.R1.fastq.gz,HN6_IgG_rabbit_negative_control_1.R1.fastq.gz
 VS586.R2.fastq.gz,HN6_IgG_rabbit_negative_control_1.R2.fastq.gz
 VS591.R1.fastq.gz,53_H3K4me3_1.R1.fastq.gz
@@ -28,7 +37,8 @@ VS592.R2.fastq.gz,53_H3K4me3_2.R2.fastq.gz
 VS588.R1.fastq.gz,HN6_H3K4me3_1.R1.fastq.gz
 VS588.R2.fastq.gz,HN6_H3K4me3_1.R2.fastq.gz
 
-# subset each of the samples 
+# subset each of the samples
+
 fq_original_loc="/data/CCBR/projects/ccbr1155/CS031014/fastq";\
 test_loc="/data/CCBR_Pipeliner/Pipelines/CARLISLE_dev/.test";\
 fq_list=("HN6_IgG_rabbit_negative_control_1.R1.fastq.gz" "HN6_IgG_rabbit_negative_control_1.R2.fastq.gz" "HN6_H3K4me3_1.R1.fastq.gz" "HN6_H3K4me3_1.R2.fastq.gz" "HN6_H3K4me3_2.R1.fastq.gz" "HN6_H3K4me3_2.R2.fastq.gz" "53_H3K4me3_1.R1.fastq.gz" "53_H3K4me3_1.R2.fastq.gz" "53_H3K4me3_2.R1.fastq.gz" "53_H3K4me3_2.R2.fastq.gz" "HN6_H4K20me3_1.R1.fastq.gz" "HN6_H4K20me3_1.R2.fastq.gz" "HN6_H4K20me3_2.R1.fastq.gz" "HN6_H4K20me3_2.R2.fastq.gz" "53_H4K20m3_1.R1.fastq.gz" "53_H4K20m3_1.R2.fastq.gz" "53_H4K20m3_2.R1.fastq.gz" "53_H4K20m3_2.R2.fastq.gz");\

.test/config_lint.yaml

@@ -12,20 +12,20 @@ samplemanifest: "/opt2/.test/samples.test_lintr.tsv"
 #####################################################################################
 # run sample contrasts
 run_contrasts: true
-contrasts: "/opt2/.test/contrasts.test.tsv"  # run_contrasts needs to be "Y"
+contrasts: "/opt2/.test/contrasts.test.tsv" # run_contrasts needs to be "Y"
 contrasts_fdr_cutoff: 0.05
 contrasts_lfc_cutoff: 0.59 # FC of 1.5
 run_go_enrichment: true
 run_rose: true
 
 # reference
-genome: "hg38"    # currently supports hg38, hg19 and mm10. Custom genome can be added with appropriate additions to "reference" section below.
+genome: "hg38" # currently supports hg38, hg19 and mm10. Custom genome can be added with appropriate additions to "reference" section below.
 
 # alignment quality threshold
 mapping_quality: 2 #only report alignment records with mapping quality of at least N (>= N).
 
 # normalization method
-## spikein: normalization will be performed based off of spike-in aligned read count; 
+## spikein: normalization will be performed based off of spike-in aligned read count;
 ## library: library normalization will be performed
 ## none: no norm will be performed
 norm_method: "spikein" # method of normalization to be used; currently supports ["spikein","library","none"]
@@ -100,7 +100,7 @@ geneset_id: "GOBP" # ["GOBP" "GOCC" "GOMF" "KEGG"]
 
 #####################################################################################
 # References
-# NOTE: "gtf" is only required if TxDb is not avaiable for the species in 
+# NOTE: "gtf" is only required if TxDb is not avaiable for the species in
 # Bioconductor eg. hs1
 #####################################################################################
 # references:
@@ -152,4 +152,4 @@ adapters: "/opt2/output_carlisle/annotation/adapters.fa"
 # R Packages
 #####################################################################################
 Rlib_dir: "/data/CCBR_Pipeliner/db/PipeDB/Rlibrary_4.3_carlisle/"
-Rpkg_config: "/opt2/output_carlisle/config//Rpack.config"
+Rpkg_config: "/opt2/output_carlisle/config//Rpack.config"

.test/contrasts.test.tsv

@@ -1,2 +1,2 @@
 condition1	condition2
-53_H3K4me3	HN6_H3K4me3
+53_H3K4me3	HN6_H3K4me3

.test/samples.test.tsv

@@ -2,4 +2,4 @@ sampleName	replicateNumber	isControl	controlName	controlReplicateNumber	path_to_
 53_H3K4me3	1	N	HN6_IgG_rabbit_negative_control	1	PIPELINE_HOME/.test/53_H3K4me3_1.R1.fastq.gz	PIPELINE_HOME/.test/53_H3K4me3_1.R2.fastq.gz
 53_H3K4me3	2	N	HN6_IgG_rabbit_negative_control	1	PIPELINE_HOME/.test/53_H3K4me3_2.R1.fastq.gz	PIPELINE_HOME/.test/53_H3K4me3_2.R2.fastq.gz
 HN6_H3K4me3	1	N	HN6_IgG_rabbit_negative_control	1	PIPELINE_HOME/.test/HN6_H3K4me3_1.R1.fastq.gz	PIPELINE_HOME/.test/HN6_H3K4me3_1.R2.fastq.gz
-HN6_IgG_rabbit_negative_control	1	Y	-	-	PIPELINE_HOME/.test/HN6_IgG_rabbit_negative_control_1.R1.fastq.gz	PIPELINE_HOME/.test/HN6_IgG_rabbit_negative_control_1.R2.fastq.gz
+HN6_IgG_rabbit_negative_control	1	Y	-	-	PIPELINE_HOME/.test/HN6_IgG_rabbit_negative_control_1.R1.fastq.gz	PIPELINE_HOME/.test/HN6_IgG_rabbit_negative_control_1.R2.fastq.gz

.test/samples.test_lintr.tsv

@@ -2,4 +2,4 @@ sampleName	replicateNumber	isControl	controlName	controlReplicateNumber	path_to_
 53_H3K4me3	1	N	HN6_IgG_rabbit_negative_control	1	/opt2/.test/53_H3K4me3_1.R1.fastq.gz	/opt2/.test/53_H3K4me3_1.R2.fastq.gz
 53_H3K4me3	2	N	HN6_IgG_rabbit_negative_control	1	/opt2/.test/53_H3K4me3_2.R1.fastq.gz	/opt2/.test/53_H3K4me3_2.R2.fastq.gz
 HN6_H3K4me3	1	N	HN6_IgG_rabbit_negative_control	1	/opt2/.test/HN6_H3K4me3_1.R1.fastq.gz	/opt2/.test/HN6_H3K4me3_1.R2.fastq.gz
-HN6_IgG_rabbit_negative_control	1	Y	-	-	/opt2/.test/HN6_IgG_rabbit_negative_control_1.R1.fastq.gz	/opt2/.test/HN6_IgG_rabbit_negative_control_1.R2.fastq.gz
+HN6_IgG_rabbit_negative_control	1	Y	-	-	/opt2/.test/HN6_IgG_rabbit_negative_control_1.R1.fastq.gz	/opt2/.test/HN6_IgG_rabbit_negative_control_1.R2.fastq.gz

CHANGELOG.md

@@ -1,25 +1,32 @@
 ## CARLISLE development version
 
-- Bug fixes: (#127, @epehrsson)
-    - Removes single-sample group check for DESeq.
-    - Increases memory for DESeq.
-    - Ensures control replicate number is an integer.
-    - Fixes FDR cutoff misassigned to log2FC cutoff.
-    - Fixes `no_dedup` variable names in library normalization scripts.
-    - Fig bug that added nonexistent directories to the singularity bind paths. (#135, @kelly-sovacool)
-- New features:
-    - Containerize rules that require R (`deseq`, `go_enrichment`, and `spikein_assessment`) to fix installation issues with common R library path. (#129, @kelly-sovacool)
-        - The `Rlib_dir` and `Rpkg_config` config options have been removed as they are no longer needed.
-    - New visualizations: (#132, @epehrsson)
-        - New rules `cov_correlation`, `homer_enrich`, `combine_homer`, `count_peaks`
-        - Add peak caller to MACS2 peak xls filename
-    - New parameters in the config file to make certain rules optional: (#133, @kelly-sovacool)
-        - GO enrichment is controlled by `run_go_enrichment` (default: `false`)
-        - ROSE is controlled by `run_rose` (default: `false`)
-- Misc:
-    - The singularity version is no longer specified, per request of the biowulf admins. (#139, @kelly-sovacool)
+### Bug fixes
+
+- Bug fixes for DESeq (#127, @epehrsson)
+  - Removes single-sample group check for DESeq.
+  - Increases memory for DESeq.
+  - Ensures control replicate number is an integer.
+  - Fixes FDR cutoff misassigned to log2FC cutoff.
+  - Fixes `no_dedup` variable names in library normalization scripts.
+- Fig bug that added nonexistent directories to the singularity bind paths. (#135, @kelly-sovacool)
+  - Containerize rules that require R (`deseq`, `go_enrichment`, and `spikein_assessment`) to fix installation issues with common R library path. (#129, @kelly-sovacool)
+    - The `Rlib_dir` and `Rpkg_config` config options have been removed as they are no longer needed.
+
+### New features
+
+- New visualizations: (#132, @epehrsson)
+  - New rules `cov_correlation`, `homer_enrich`, `combine_homer`, `count_peaks`
+  - Add peak caller to MACS2 peak xls filename
+- New parameters in the config file to make certain rules optional: (#133, @kelly-sovacool)
+  - GO enrichment is controlled by `run_go_enrichment` (default: `false`)
+  - ROSE is controlled by `run_rose` (default: `false`)
+
+### Misc
+
+- The singularity version is no longer specified, per request of the biowulf admins. (#139, @kelly-sovacool)
 
 ## CARLISLE v2.5.0
+
 - Refactors R packages to a common source location (#118, @slsevilla)
 - Adds a --force flag to allow for re-initialization of a workdir (#97, @slsevilla)
 - Fixes error with testrun in DESEQ2 (#113, @slsevilla)
@@ -30,31 +37,36 @@
 - Minor documentation improvements. (#100, @kelly-sovacool)
 - Fix: allow printing the version or help message even if singularity is not in the path. (#110, @kelly-sovacool)
 
-## CARLISLE v2.4.1 
+## CARLISLE v2.4.1
+
 - Add GitHub Action to add issues/PRs to personal project boards by @kelly-sovacool in #95
 - Create install script by @kelly-sovacool in #93
 - feat: use summits bed for homer input; save temporary files; fix deseq2 bug by @slsevilla in #108
 - docs: adding citation and DOI to pipeline by @slsevilla in #107
 - Test a dryrun with GitHub Actions by @kelly-sovacool in #94
 
 ## CARLISLE v2.4.0
+
 - Feature- Merged Yue's fork, adding DEEPTOOLS by @slsevilla in #85
 - Feature- Added tracking features from SPOOK by @slsevilla in #88
 - Feature - Dev test run completed by @slsevilla in #89
 - Bug - Fixed bugs related to Biowulf transition
 
 ## CARLISLE v2.1.0
+
 - enhancement
 - update gopeaks resources
 - change SEACR to run "norm" without spikein controls, "non" with spikein controls
 - update docs for changes; provide extra troubleshooting guidance
 - fix GoEnrich bug for failed plots
 
 ## CARLISLE v2.0.1
+
 - fix error when contrasts set to "N"
 - adjust goenrich resources to be more efficient
 
 ## CARLISLE 2.0.0
+
 - Add a MAPQ filter to samtools (rule align)
 - Add GoPeaks MultiQC module
 - Allow for library normalization to occur during first pass
@@ -71,16 +83,20 @@
 - moved ~12% of all jobs to local deployment (within SLURM submission)
 
 ## CARLISLE 1.2.0
+
 - merge increases to resources; update workflow img, contributions
 
 ## CARLISLE 1.1.1
+
 - patch for gz bigbed bug
 
 ## CARLISLE 1.1.0
+
 - add broad-cutoff to macs2 broad peaks param settings
 - add non.stringent and non.relaxed to annotation options
 - merge DESEQ and DESEQ2 rules together
 - identify some files as temp
 
 ## CARLISLE 1.0.1
+
 - contains patch for DESEQ error with non hs1 reference samples

annotation/README.md

@@ -1,9 +1,11 @@
 ## mm10 download
+
 https://bitbucket.org/young_computation/rose/src/master/annotation/mm10_refseq.ucsc
 
 `create_hs1_ucsc.sh` script was used to create the hs1 ucsc file.
 
 #### hg19_refseq.ucsc and hg38_refseq.ucsc source
+
 /data/khanlab3/gb_omics/processed_DATA/YueHu/cutrun_120822# hg19_refseq.ucsc and hg38_refseq.ucsc source
 
 # info on these resources is outlined in: https://github.com/CCBR/CARLISLE/issues/27

annotation/create_hs1_uscs.sh

@@ -3,4 +3,4 @@
 module load ucsc
 gtfToGenePred -genePredExt -ignoreGroupsWithoutExons /data/CCBR_Pipeliner/db/PipeDB/Indices/hs1/genes.gtf hs1.genes.genePred
 head -n1 hg19_refseq.ucsc > hs1.ucsc
-awk -F"\t" -v OFS="\t" '{print $NF,$_}' hs1.genes.genePred >> hs1.ucsc
+awk -F"\t" -v OFS="\t" '{print $NF,$_}' hs1.genes.genePred >> hs1.ucsc

bin/carlisle

@@ -5,4 +5,4 @@ SCRIPTDIRNAME=$(readlink -f $(dirname "$SCRIPTNAME"))
 TOOLDIR=$(dirname "$SCRIPTDIRNAME")
 TOOLNAME=$(basename "$SCRIPTNAME")
 
-${TOOLDIR}/carlisle "$@" || true
+${TOOLDIR}/carlisle "$@" || true