Merge pull request #158 from drpatelh/master

Close issues and aesthetic updates

Author: drpatelh

.github/workflows/awstest.yml

@@ -6,11 +6,13 @@ on:
   push:
     branches:
       - master
+      - dev
   release:
     types: [published]
 
 jobs:
   run-awstest:
+    if: github.repository == 'nf-core/chipseq'
     name: Run AWS test
     runs-on: ubuntu-latest
     steps:
@@ -26,5 +28,10 @@ jobs:
           AWS_ACCESS_KEY_ID: ${{secrets.AWS_KEY_ID}}
           AWS_SECRET_ACCESS_KEY: ${{secrets.AWS_KEY_SECRET}}
           TOWER_ACCESS_TOKEN: ${{secrets.TOWER_ACCESS_TOKEN}}
-        run: |
-          aws batch submit-job --region eu-west-1 --job-name nf-core-chipseq --job-queue 'default-8b3836e0-5eda-11ea-96e5-0a2c3f6a2a32' --job-definition nextflow --container-overrides '{"command": ["nf-core/chipseq", "-r '"${GITHUB_SHA}"' -profile test_full --outdir s3://nf-core-awsmegatests/chipseq/results-'"${GITHUB_SHA}"' -w s3://nf-core-awsmegatests/chipseq/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
+        run: | # Submits job to AWS batch using a 'nextflow-4GiB' instance. Setting JVM options to "-XX:+UseG1GC" for more efficient garbage collection when staging remote files.
+          aws batch submit-job \
+          --region eu-west-1 \
+          --job-name nf-core-chipseq \
+          --job-queue 'default-8b3836e0-5eda-11ea-96e5-0a2c3f6a2a32' \
+          --job-definition nextflow-4GiB \
+          --container-overrides '{"command": ["nf-core/chipseq", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://nf-core-awsmegatests/chipseq/results-'"${GITHUB_SHA}"' -w s3://nf-core-awsmegatests/chipseq/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}, {"name": "NXF_OPTS", "value": "-XX:+UseG1GC"}]}'

CHANGELOG.md

@@ -8,14 +8,19 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ### `Added`
 
 * [#138](https://github.com/nf-core/chipseq/issues/138) - Add social preview image
+* [#153](https://github.com/nf-core/chipseq/issues/153) - Add plotHeatmap
 * [nf-core/atacseq#63](https://github.com/nf-core/atacseq/issues/63) - Added multicore support for Trim Galore!
 * [nf-core/atacseq#71](https://github.com/nf-core/atacseq/issues/71) - consensus_peaks.mLb.clN.boolean.intersect.plot.pdf not generated
 * [nf-core/atacseq#75](https://github.com/nf-core/atacseq/issues/75) - Include gene annotation versions in multiqc report
 * [nf-core/atacseq#76](https://github.com/nf-core/atacseq/issues/76) - featureCounts coupled to DESeq2
 * [nf-core/atacseq#79](https://github.com/nf-core/atacseq/issues/79) - Parallelize DESeq2
 * [nf-core/atacseq#97](https://github.com/nf-core/atacseq/issues/97) - PBC1, PBC2 from pipeline?
 * Update template to tools `1.9`
+* Replace `set` with `tuple` and `file()` with `path()` in all processes
+* Capitalise process names
 * Parameters:
+  * `--skip_peak_qc` to skip MACS2 peak QC plot generation
+  * `--skip_peak_annotation` to skip annotation of MACS2 and consensus peaks with HOMER
   * `--skip_consensus_peaks` to skip consensus peak generation
   * `--deseq2_vst` to use variance stabilizing transformation (VST) instead of regularized log transformation (rlog) with DESeq2
   * `--publish_dir_mode` to customise method of publishing results to output directory [nf-core/tools#585](https://github.com/nf-core/tools/issues/585)
@@ -24,6 +29,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 * [#118](https://github.com/nf-core/chipseq/issues/118) - Running on with SGE
 * [#132](https://github.com/nf-core/chipseq/issues/132) - BigWig Error: sort: cannot create temporary file in '': Read-only file system
+* [#154](https://github.com/nf-core/chipseq/issues/154) - computeMatrix.val.mat.gz files not zipped
 * [nf-core/atacseq#73](https://github.com/nf-core/atacseq/issues/73) - macs_annotatePeaks.mLb.clN.summary.txt file is not created
 * [nf-core/atacseq#86](https://github.com/nf-core/atacseq/issues/86) - bug in the plot_homer_annotatepeaks.r script
 * [nf-core/atacseq#102](https://github.com/nf-core/atacseq/issues/102) - Incorrect Group ID assigned by featurecounts_deseq2.r

conf/base.config

@@ -38,6 +38,9 @@ process {
   withLabel:process_long {
     time = { check_max( 20.h * task.attempt, 'time' ) }
   }
+  withLabel:error_ignore {
+    errorStrategy = 'ignore'
+  }
   withName:get_software_versions {
     cache = false
   }

conf/test.config

@@ -28,8 +28,4 @@ params {
 
   // For speed to avoid CI time-out
   fingerprint_bins = 100
-
-  // Tests fail without this:
-  // ERROR: Max count before zero is les than min required count (4), sample not sufficiently deep or duplicates removed
-  skip_preseq = true
 }

docs/output.md

@@ -151,7 +151,7 @@ The library-level alignments associated with the same sample are merged and subs
     * `bwa/mergedLibrary/deepTools/plotFingerprint/`  
       * Output files: `*.plotFingerprint.pdf`, `*.plotFingerprint.qcmetrics.txt`, `*.plotFingerprint.raw.txt`
     * `bwa/mergedLibrary/deepTools/plotProfile/`  
-      * Output files: `*.computeMatrix.mat.gz`, `*.computeMatrix.vals.mat.gz`, `*.plotProfile.pdf`, `*.plotProfile.tab`.
+      * Output files: `*.computeMatrix.mat.gz`, `*.computeMatrix.vals.mat.tab`, `*.plotProfile.pdf`, `*.plotProfile.tab`, `*.plotHeatmap.pdf`, `*.plotHeatmap.mat.tab`.
 
 4. **Call peaks**
 

docs/usage.md

@@ -38,6 +38,8 @@
   * [`--broad_cutoff`](#--broad_cutoff)
   * [`--min_reps_consensus`](#--min_reps_consensus)
   * [`--save_macs_pileup`](#--save_macs_pileup)
+  * [`--skip_peak_qc`](#--skip_peak_qc)
+  * [`--skip_peak_annotation`](#--skip_peak_annotation)
   * [`--skip_consensus_peaks`](#--skip_consensus_peaks)
 * [Differential analysis](#differential_analysis)
   * [`--deseq2_vst`](#--deseq2_vst)
@@ -408,6 +410,14 @@ Number of biological replicates required from a given condition for a peak to co
 
 Instruct MACS2 to create bedGraph files using the `-B --SPMR` parameters.
 
+### `--skip_peak_qc`
+
+Skip MACS2 peak QC plot generation.
+
+### `--skip_peak_annotation`
+
+Skip annotation of MACS2 and consensus peaks with HOMER.
+
 ### `--skip_consensus_peaks`
 
 Skip consensus peak generation, annotation and counting.