kerimoff · olgabot · May 2, 2019 · May 2, 2019 · May 2, 2019 · May 2, 2019
diff --git a/.travis.yml b/.travis.yml
@@ -8,19 +8,17 @@ matrix:
   fast_finish: true
 
 before_install:
-  # PRs to master are only ok if coming from dev branch
-  - '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && [ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ])'
   # Pull the docker image first so the test doesn't wait for this
-  - docker pull nfcore/rnaseq:dev
+  - docker pull czbiohub/rnaseq
   # Fake the tag locally so that the pipeline runs properly
-  - docker tag nfcore/rnaseq:dev nfcore/rnaseq:1.2
+  - docker tag czbiohub/rnaseq czbiohub/rnaseq:1.2
 
 install:
   # Install Nextflow
   - mkdir /tmp/nextflow && cd /tmp/nextflow
   - wget -qO- get.nextflow.io | bash
   - sudo ln -s /tmp/nextflow/nextflow /usr/local/bin/nextflow
-  # Install nf-core/tools
+  # Install czbiohub/tools
   - pip install nf-core
   # Reset
   - mkdir ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}/tests
@@ -30,8 +28,6 @@ env:
   - NXF_VER='' # Plus: get the latest NF version and check that it works
 
 script:
-  # Lint the pipeline code
-  - "nf-core lint ${TRAVIS_BUILD_DIR}"
   # Run, build reference genome with STAR
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker
   # Run, build reference genome with HISAT2

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,24 +1,31 @@
-# nf-core/rnaseq
+# czbiohub/rnaseq
 
-## [Version 1.2](https://github.com/nf-core/rnaseq/releases/tag/1.2) - 2018-12-12
+## [Version 2.0](https://github.com/czbiohub/rnaseq/releases/tag/2.0) - TBA
+
+#### Pipeline updates
+
+- Replaced TrimGalore! with fastp
+- Replaced featureCounts with htseq-count
+
+## [Version 1.2](https://github.com/czbiohub/rnaseq/releases/tag/1.2) - 2018-12-12
 
 #### Pipeline updates
 * Removed some outdated documentation about non-existent features
 * Config refactoring and code cleaning
 * Added a `--fcExtraAttributes` option to specify more than ENSEMBL gene names in `featureCounts`
-* Remove legacy rseqc `strandRule` config code. [#119](https://github.com/nf-core/rnaseq/issues/119)
-* Added STRINGTIE ballgown output to results folder [#125](https://github.com/nf-core/rnaseq/issues/125)
+* Remove legacy rseqc `strandRule` config code. [#119](https://github.com/czbiohub/rnaseq/issues/119)
+* Added STRINGTIE ballgown output to results folder [#125](https://github.com/czbiohub/rnaseq/issues/125)
 * HiSAT index build now requests `200GB` memory, enough to use the exons / splice junction option for building.
   * Added documentation about the `--hisatBuildMemory` option.
-* BAM indices are stored and re-used between processes [#71](https://github.com/nf-core/rnaseq/issues/71)
+* BAM indices are stored and re-used between processes [#71](https://github.com/czbiohub/rnaseq/issues/71)
 
 #### Bug Fixes
-* Fixed conda bug which caused problems with environment resolution due to changes in bioconda [#113](https://github.com/nf-core/rnaseq/issues/113)
-* Fixed wrong gffread command line [#117](https://github.com/nf-core/rnaseq/issues/117)
-* Added `cpus = 1` to `workflow summary process` [#130](https://github.com/nf-core/rnaseq/issues/130)
+* Fixed conda bug which caused problems with environment resolution due to changes in bioconda [#113](https://github.com/czbiohub/rnaseq/issues/113)
+* Fixed wrong gffread command line [#117](https://github.com/czbiohub/rnaseq/issues/117)
+* Added `cpus = 1` to `workflow summary process` [#130](https://github.com/czbiohub/rnaseq/issues/130)
 
 
-## [Version 1.1](https://github.com/nf-core/rnaseq/releases/tag/1.1) - 2018-10-05
+## [Version 1.1](https://github.com/czbiohub/rnaseq/releases/tag/1.1) - 2018-10-05
 
 #### Pipeline updates
 * Wrote docs and made minor tweaks to the `--skip_qc` and associated options
@@ -28,25 +35,25 @@
 * Updated minimum nextflow version to `0.32.0`
 
 #### Bug Fixes
-* [#77](https://github.com/nf-core/rnaseq/issues/77): Added back `executor = 'local'` for the `workflow_summary_mqc`
-* [#95](https://github.com/nf-core/rnaseq/issues/95): Check if task.memory is false instead of null
-* [#97](https://github.com/nf-core/rnaseq/issues/97): Resolved edge-case where numeric sample IDs are parsed as numbers causing some samples to be incorrectly overwritten.
+* [#77](https://github.com/czbiohub/rnaseq/issues/77): Added back `executor = 'local'` for the `workflow_summary_mqc`
+* [#95](https://github.com/czbiohub/rnaseq/issues/95): Check if task.memory is false instead of null
+* [#97](https://github.com/czbiohub/rnaseq/issues/97): Resolved edge-case where numeric sample IDs are parsed as numbers causing some samples to be incorrectly overwritten.
 
 
-## [Version 1.0](https://github.com/nf-core/rnaseq/releases/tag/1.0) - 2018-08-20
+## [Version 1.0](https://github.com/czbiohub/rnaseq/releases/tag/1.0) - 2018-08-20
 
 This release marks the point where the pipeline was moved from [SciLifeLab/NGI-RNAseq](https://github.com/SciLifeLab/NGI-RNAseq)
-over to the new [nf-core](http://nf-co.re/) community, at [nf-core/rnaseq](https://github.com/nf-core/rnaseq).
+over to the new [czbiohub](http://nf-co.re/) community, at [czbiohub/rnaseq](https://github.com/czbiohub/rnaseq).
 
 View the previous changelog at [SciLifeLab/NGI-RNAseq/CHANGELOG.md](https://github.com/SciLifeLab/NGI-RNAseq/blob/master/CHANGELOG.md)
 
-In addition to porting to the new nf-core community, the pipeline has had a number of major changes in this version.
+In addition to porting to the new czbiohub community, the pipeline has had a number of major changes in this version.
 There have been 157 commits by 16 different contributors covering 70 different files in the pipeline: 7,357 additions and 8,236 deletions!
 
 In summary, the main changes are:
 
-* Rebranding and renaming throughout the pipeline to nf-core
-* Updating many parts of the pipeline config and style to meet nf-core standards
+* Rebranding and renaming throughout the pipeline to czbiohub
+* Updating many parts of the pipeline config and style to meet czbiohub standards
 * Support for GFF files in addition to GTF files
     * Just use `--gff` instead of `--gtf` when specifying a file path
 * New command line options to skip various quality control steps

diff --git a/Dockerfile b/Dockerfile
@@ -1,8 +1,13 @@
 FROM nfcore/base
-MAINTAINER Phil Ewels <[email protected]>
-LABEL authors="[email protected]" \
-    description="Docker image containing all requirements for the nfcore/rnaseq pipeline"
+MAINTAINER Olga Botvinnik <[email protected]>
+LABEL authors="[email protected]" \
+    description="Docker image containing all requirements for the czbiohub/rnaseq pipeline"
 
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nf-core-rnaseq-1.2/bin:$PATH
+ENV PATH /opt/conda/envs/czbiohub-rnaseq-1.2/bin:$PATH
+
+ENV PACKAGES pigz
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
diff --git a/Makefile b/Makefile
@@ -0,0 +1,49 @@
+
+test: test_hisat
+
+test_hisat:
+	nextflow run -profile test,docker main.nf -ansi-log false -resume --aligner hisat2
+
+test_biohub:
+	nextflow run main.nf \
+		-latest \
+		--reads "s3://olgabot-maca/mini-maca/*{R1,R2}*.fastq.gz" \
+		--genome GRCm38,ERCC \
+		-profile czbiohub_aws \
+		--saveReference \
+		--saveTrimmed \
+		--saveAlignedIntermediates \
+		--run_splicing_exp_quant \
+		--run_exon_quant \
+		-dump-channels \
+		--outdir "s3://olgabot-maca/mini-maca/results" \
+		-resume
+
+test_biohub_hisat:
+	nextflow run main.nf \
+		-latest \
+		--reads "s3://olgabot-maca/mini-maca/*{R1,R2}*.fastq.gz" \
+		--genome GRCm38,ERCC \
+		-profile czbiohub_aws \
+		--saveReference \
+		--saveTrimmed \
+		--saveAlignedIntermediates \
+		--run_splicing_exp_quant \
+		--run_exon_quant \
+		-dump-channels \
+		--outdir "s3://olgabot-maca/mini-maca/results" \
+		-resume --aligner hisat2
+
+
+docker: docker_build docker_push
+
+docker_build:
+	@docker build \
+		--build-arg VCS_REF=`git rev-parse --short HEAD`  \
+		--build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \
+		-t czbiohub/rnaseq .
+
+docker_push:
+	sudo docker login
+	sudo docker push czbiohub/rnaseq
+	docker images
diff --git a/README.md b/README.md
@@ -1,28 +1,28 @@
-# ![nfcore/rnaseq](docs/images/nfcore-rnaseq_logo.png)
+# ![czbiohub/rnaseq](docs/images/czbiohub-rnaseq_logo.png)
 
-[![Build Status](https://travis-ci.org/nf-core/rnaseq.svg?branch=master)](https://travis-ci.org/nf-core/rnaseq)
+[![Build Status](https://travis-ci.org/czbiohub/rnaseq.svg?branch=master)](https://travis-ci.org/czbiohub/rnaseq)
 [![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.32.0-brightgreen.svg)](https://www.nextflow.io/)
 [![DOI](https://zenodo.org/badge/127293091.svg)](https://zenodo.org/badge/latestdoi/127293091)
-[![Gitter](https://img.shields.io/badge/gitter-%20join%20chat%20%E2%86%92-4fb99a.svg)](https://gitter.im/nf-core/Lobby)
+[![Gitter](https://img.shields.io/badge/gitter-%20join%20chat%20%E2%86%92-4fb99a.svg)](https://gitter.im/czbiohub/Lobby)
 
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/)
-[![Docker Container available](https://img.shields.io/docker/automated/nfcore/rnaseq.svg)](https://hub.docker.com/r/nfcore/rnaseq/)
+[![Docker Container available](https://img.shields.io/docker/automated/czbiohub/rnaseq.svg)](https://hub.docker.com/r/czbiohub/rnaseq/)
 ![Singularity Container available](
 https://img.shields.io/badge/singularity-available-7E4C74.svg)
 
 
 ### Introduction
 
-**nfcore/rnaseq** is a bioinformatics analysis pipeline used for RNA sequencing data.
+**czbiohub/rnaseq** is a bioinformatics analysis pipeline used for RNA sequencing data.
 
-The workflow processes raw data from FastQ inputs ([FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), [Trim Galore!](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)), aligns the reads ([STAR](https://github.com/alexdobin/STAR) or [HiSAT2](https://ccb.jhu.edu/software/hisat2/index.shtml)), generates gene counts ([featureCounts](http://bioinf.wehi.edu.au/featureCounts/), [StringTie](https://ccb.jhu.edu/software/stringtie/)) and performs extensive quality-control on the results ([RSeQC](http://rseqc.sourceforge.net/), [dupRadar](https://bioconductor.org/packages/release/bioc/html/dupRadar.html), [Preseq](http://smithlabresearch.org/software/preseq/), [edgeR](https://bioconductor.org/packages/release/bioc/html/edgeR.html), [MultiQC](http://multiqc.info/)). See the [output documentation](docs/output.md) for more details of the results.
+The workflow processes raw data from FastQ inputs ([FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), [fastp](https://github.com/OpenGene/fastp)), aligns the reads ([STAR](https://github.com/alexdobin/STAR) or [HiSAT2](https://ccb.jhu.edu/software/hisat2/index.shtml)), generates gene counts ([htseq-count](https://htseq.readthedocs.io/en/release_0.11.1/count.html), [StringTie](https://ccb.jhu.edu/software/stringtie/)) and performs extensive quality-control on the results ([RSeQC](http://rseqc.sourceforge.net/), [dupRadar](https://bioconductor.org/packages/release/bioc/html/dupRadar.html), [Preseq](http://smithlabresearch.org/software/preseq/), [edgeR](https://bioconductor.org/packages/release/bioc/html/edgeR.html), [MultiQC](http://multiqc.info/)). See the [output documentation](docs/output.md) for more details of the results.
 
 Additionally, the pipeline is expanded to be able to quantify transcript, exon, alternative splicing and TxRevise expressions. See [optional quantification methods](docs/extra_phenotype_quantification.md) for details.
 
 The pipeline is built using [Nextflow](https://www.nextflow.io), a bioinformatics workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.
 
 ### Documentation
-The nfcore/rnaseq pipeline comes with documentation about the pipeline, found in the `docs/` directory:
+The czbiohub/rnaseq pipeline comes with documentation about the pipeline, found in the `docs/` directory:
 
 1. [Installation](docs/installation.md)
 2. Pipeline configuration
@@ -38,12 +38,12 @@ The nfcore/rnaseq pipeline comes with documentation about the pipeline, found in
 5. [Output and how to interpret the results](docs/output.md)
 6. [Troubleshooting](docs/troubleshooting.md)
 
-### General overview 
+### General overview
 The schema shown below represents the high level structure of the pipeline.
-# ![nfcore/rnaseq](docs/images/pipeline_high_level_schema.svg)
+# ![czbiohub/rnaseq](docs/images/pipeline_high_level_schema.svg)
 
 ### Credits
-These scripts were originally written for use at the [National Genomics Infrastructure](https://portal.scilifelab.se/genomics/), part of [SciLifeLab](http://www.scilifelab.se/) in Stockholm, Sweden, by Phil Ewels ([@ewels](https://github.com/ewels)) and Rickard Hammarén ([@Hammarn](https://github.com/Hammarn)).
+These scripts were originally written for use at the [National Genomics Infrastructure](https://portal.scilifelab.se/genomics/), part of [SciLifeLab](http://www.scilifelab.se/) in Stockholm, Sweden, by Phil Ewels ([@ewels](https://github.com/ewels)) and Rickard Hammarén ([@Hammarn](https://github.com/Hammarn)). They have since taken on a life of their own at Chan Zuckerberg Biohub where they are maintained by Olga Botvinnik.
 
 Many thanks to other who have helped out along the way too, including (but not limited to):
 [@Galithil](https://github.com/Galithil),

diff --git a/Singularity b/Singularity
@@ -1,13 +1,13 @@
-From:nfcore/base
+From:czbiohub/base
 Bootstrap:docker
 
 %labels
     MAINTAINER Phil Ewels <[email protected]>
-    DESCRIPTION Singularity image containing all requirements for the nf-core/rnaseq pipeline
+    DESCRIPTION Singularity image containing all requirements for the czbiohub/rnaseq pipeline
     VERSION 1.2
 
 %environment
-    PATH=/opt/conda/envs/nf-core-rnaseq-1.2/bin:$PATH
+    PATH=/opt/conda/envs/czbiohub-rnaseq-1.2/bin:$PATH
     export PATH
 
 %files

diff --git a/assets/biotypes_header.txt b/assets/biotypes_header.txt
@@ -1,11 +1,11 @@
 # id: 'biotype-counts'
 # section_name: 'Biotype Counts'
 # description: "shows reads overlapping genomic features of different biotypes,
-#     counted by <a href='http://bioinf.wehi.edu.au/featureCounts'>featureCounts</a>."
+#     counted by <a href='https://htseq.readthedocs.io/en/release_0.11.1/count.html'>htseq-count</a>."
 # plot_type: 'bargraph'
-# anchor: 'featurecounts_biotype'
+# anchor: 'htseqcount_biotype'
 # pconfig:
-#     id: "featureCounts_biotype_plot"
-#     title: "featureCounts: Biotypes"
+#     id: "htseqcount_biotype_plot"
+#     title: "htseqcount: Biotypes"
 #     xlab: "# Reads"
 #     cpswitch_counts_label: "Number of Reads"
diff --git a/assets/email_template.html b/assets/email_template.html
@@ -5,21 +5,21 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge">
   <meta name="viewport" content="width=device-width, initial-scale=1">
 
-  <meta name="description" content="nfcore/rnaseq: a bioinformatics best-practice analysis pipeline used for RNA sequencing data at the National Genomics Infrastructure at SciLifeLab Stockholm, Sweden.">
-  <title>nfcore/rnaseq Pipeline Report</title>
+  <meta name="description" content="czbiohub/rnaseq: a bioinformatics best-practice analysis pipeline used for RNA sequencing data at the National Genomics Infrastructure at SciLifeLab Stockholm, Sweden.">
+  <title>czbiohub/rnaseq Pipeline Report</title>
 </head>
 <body>
 <div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
 
-<img src="cid:nfcorernaseqlogo">
+<img src="cid:czbiohubrnaseqlogo">
 
-<h1>nfcore/rnaseq: version ${version}</h1>
+<h1>czbiohub/rnaseq: version ${version}</h1>
 <h2>Run Name: $runName</h2>
 
 <% if (!success){
     out << """
     <div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
-        <h4 style="margin-top:0; color: inherit;">nfcore/rnaseq execution completed unsuccessfully!</h4>
+        <h4 style="margin-top:0; color: inherit;">czbiohub/rnaseq execution completed unsuccessfully!</h4>
         <p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p>
         <p>The full error message was:</p>
         <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${errorReport}</pre>
@@ -28,7 +28,7 @@ <h4 style="margin-top:0; color: inherit;">nfcore/rnaseq execution completed unsu
 } else if(skipped_poor_alignment.size() > 0) {
     out << """
     <div style="color: #856404; background-color: #fff3cd; border-color: #ffeeba; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
-        <h4 style="margin-top:0; color: inherit;">nfcore/rnaseq execution completed with warnings!</h4>
+        <h4 style="margin-top:0; color: inherit;">czbiohub/rnaseq execution completed with warnings!</h4>
         <p>The pipeline finished successfully, but the following samples were skipped due to very low alignment (&lt; 5%):</p>
         <ul>
             <li><code>${skipped_poor_alignment.join('</code></li><li><code>')}</code></li>
@@ -39,7 +39,7 @@ <h4 style="margin-top:0; color: inherit;">nfcore/rnaseq execution completed with
 } else {
     out << """
     <div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
-        nfcore/rnaseq execution completed successfully!
+        czbiohub/rnaseq execution completed successfully!
     </div>
     """
 }
@@ -56,9 +56,9 @@ <h3>Pipeline Configuration:</h3>
     </tbody>
 </table>
 
-<p>nfcore/rnaseq is a bioinformatics best-practice analysis pipeline used for RNA sequencing data at the National Genomics Infrastructure at SciLifeLab Stockholm, Sweden.</p>
+<p>czbiohub/rnaseq is a bioinformatics best-practice analysis pipeline used for RNA sequencing data at the National Genomics Infrastructure at SciLifeLab Stockholm, Sweden.</p>
 <p>The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.</p>
-<p>For more information, please see the pipeline homepage: <a href="https://github.com/nf-core/rnaseq">https://github.com/nf-core/rnaseq</a></p>
+<p>For more information, please see the pipeline homepage: <a href="https://github.com/czbiohub/rnaseq">https://github.com/czbiohub/rnaseq</a></p>
 
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