Merge pull request #13 from qbic-pipelines/dev

Patch release 1.0.1

.github/workflows/ci.yml

@@ -23,7 +23,7 @@ jobs:
     strategy:
       matrix:
         # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: ['20.10.0', '']
+        nxf_ver: ['21.04.1', '']
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
@@ -42,4 +42,37 @@ jobs:
 
       - name: Run pipeline with test data
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub
+
+  test_profile:
+    name: Run workflow tests
+    # Only run on push if this is the nf-core dev branch (merged PRs)
+    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'qbic-pipelines/cellranger') }}
+    runs-on: ubuntu-20.04
+    env:
+      NXF_VER: ${{ matrix.nxf_ver }}
+      NXF_ANSI_LOG: false
+    strategy:
+      matrix:
+        # Nextflow versions: check pipeline minimum and current latest
+        nxf_ver: ['21.04.1', '']
+        profile: ['test_genome']
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Pull docker image
+        run: |
+          docker pull qbicpipelines/cellranger:dev
+          docker tag qbicpipelines/cellranger:dev qbicpipelines/cellranger:1.0
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Run pipeline with test data
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker -stub

CHANGELOG.md

@@ -3,16 +3,20 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.0 - Mordor
-
-Initial release of qbic-pipelines/cellranger, created with the [nf-core](https://nf-co.re/) template.
+## v1.0.1 - Mordor - patch
 
 ### `Added`
 
-Updated to nf-core template v1.14.
+* Using stub feature for CI tests.
 
 ### `Fixed`
 
+* Fixed channel issues when not providing a reference file.
+
 ### `Dependencies`
 
 ### `Deprecated`
+
+## v1.0 - Mordor
+
+Initial release of qbic-pipelines/cellranger, created with the [nf-core](https://nf-co.re/) template.

README.md

@@ -2,12 +2,11 @@
 
 **Nextflow wrapper around the Cell Ranger pipeline for single cell RNAseq analysis**.
 
-[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A520.10.0-brightgreen.svg)](https://www.nextflow.io/)
-[![Docker](https://img.shields.io/docker/automated/nfcore/qbic-pipelines-cellranger.svg)](https://hub.docker.com/r/qbicpipelines/cellranger)
+[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A521.04.1-brightgreen.svg)](https://www.nextflow.io/)
+[![GitHub Actions CI Status](https://github.com/qbic-pipelines/cellranger/workflows/nf-core%20CI/badge.svg)](https://github.com/qbic-pipelines/cellranger/actions)
 
 ## Introduction
 
-<!-- TODO nf-core: Write a 1-2 sentence summary of what data the pipeline is for and what it does -->
 **qbic-pipelines/cellranger** is a Nextflow pipeline that wraps the Cell Ranger pipeline for single cell RNAseq analysis. It additionally performs QC on the Fastq files
 with `FastQC` and summarizes the QC with `MultiQC`.
 

conf/test.config

@@ -21,5 +21,4 @@ params {
   gtf = 'https://raw.githubusercontent.com/qbic-pipelines/cellranger/dev/testdata/Homo_sapiens.GRCh38.104.chr_22.gtf'
   reference_name = 'Homo_sapiens.GRCh38.chr_22'
   index_file = true
-  save_reference = true
 }

conf/test_genome.config

@@ -0,0 +1,22 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow config file for running tests
+ * -------------------------------------------------
+ * Defines bundled input files and everything required
+ * to run a fast and simple test. Use as follows:
+ *   nextflow run nf-core/qbic-pipelines-cellranger -profile test,<docker/singularity>
+ */
+
+params {
+  config_profile_name = 'Test profile'
+  config_profile_description = 'Minimal test dataset to check pipeline function'
+  // Limit resources so that this can run on GitHub Actions
+  max_cpus = 2
+  max_memory = 6.GB
+  max_time = 48.h
+
+  // Input data
+  input = 'https://raw.githubusercontent.com/qbic-pipelines/cellranger/master/testdata/input_data.tsv'
+  genome = 'GRCh38'
+  index_file = true
+}

main.nf

@@ -71,11 +71,17 @@ if (params.index_file) {
 if (params.prebuilt_reference){
     if (params.genome) exit 1, "Please provide either a reference folder or a genome name, not both."
     ch_reference_path = Channel.fromPath("${params.prebuilt_reference}")
+    ch_fasta = Channel.empty()
+    ch_gtf = Channel.empty()
 } else if (!params.genome) {
     if (!params.fasta | !params.gtf) exit 1, "Please provide either a genome reference name with the `--genome` parameter, or a reference folder, or a fasta and gtf file."
     if (params.fasta)  { ch_fasta = file(params.fasta, checkIfExists: true) } else { exit 1, "Please provide fasta file with the '--fasta' option." }
     if (params.gtf)  { ch_gtf = file(params.gtf, checkIfExists: true) } else { exit 1, "Please provide gtf file with the '--gtf' option." }
     ch_reference_path = Channel.empty()
+} else {
+    ch_fasta = Channel.empty()
+    ch_gtf = Channel.empty()
+    ch_reference_path = Channel.empty()
 }
 
 ////////////////////////////////////////////////////
@@ -291,6 +297,12 @@ process count {
             --localmem=${task.memory.toGiga()}
         """
     }
+
+    stub:
+    """
+    mkdir -p "sample-${GEM}/outs/"
+    touch sample-${GEM}/outs/fake_file.txt
+    """
 }
 
 /*

nextflow.config

@@ -9,7 +9,7 @@
 params {
 
   // Workflow flags
-  index_file = true
+  index_file = false
   input = null
   input_paths = null
   outdir = './results'
@@ -119,6 +119,7 @@ profiles {
   }
   test { includeConfig 'conf/test.config' }
   test_full { includeConfig 'conf/test_full.config' }
+  test_genome { includeConfig 'conf/test_genome.config' }
 }
 
 // Load igenomes.config if required
@@ -160,8 +161,8 @@ manifest {
   homePage = 'https://github.com/qbic-pipelines/cellranger'
   description = 'Cell ranger pipeline for single cell RNAseq'
   mainScript = 'main.nf'
-  nextflowVersion = '>=20.10.0'
-  version = '1.0dev'
+  nextflowVersion = '>=21.04.1'
+  version = '1.0.1'
 }
 
 // Function to ensure that resource requirements don't go beyond