From ecdd06b92a6fe222cd0ed91931dfc979d29dd4bb Mon Sep 17 00:00:00 2001 From: "Philip R. Kensche" Date: Wed, 6 Mar 2024 13:58:28 +0100 Subject: [PATCH 1/8] Migrated to DSL2. Additionally, changed README and use Nextflow`s default singularity conversion mechanism and container name --- README.md | 87 +++++++++++++++++++++++++++---------------------- main.nf | 84 ++++++++++++++++++++++++----------------------- nextflow.config | 6 +++- test/test1.sh | 2 +- 4 files changed, 98 insertions(+), 81 deletions(-) diff --git a/README.md b/README.md index 825a3d2..4b2b1a2 100644 --- a/README.md +++ b/README.md @@ -4,24 +4,6 @@ Convert BAM files back to FASTQ. -## Quickstart with Conda - -We do not recommend Conda for running the workflow. It may happen that packages are not available in any channels anymore and that the environment is broken. For reproducible research, please use containers. - -Provided you have a working [Conda](https://docs.conda.io/en/latest/) installation, you can run the workflow with - -```bash -mkdir test_out/ -nextflow run main.nf \ - -profile local,conda \ - -ansi-log \ - --input=/path/to/your.bam \ - --outputDir=test_out \ - --sortFastqs=false -``` - -For each BAM file in the comma-separated `--input` parameter, one directory with FASTQs is created in the `outputDir`. With the `local` profile the processing jobs will be executed locally. The `conda` profile will let Nextflow create a Conda environment from the `task-environment.yml` file. By default, the conda environment will be created in the source directory of the workflow (see [nextflow.config](https://github.com/DKFZ-ODCF/nf-bam2fastq/blob/master/nextflow.config)). - ## Quickstart with Docker Dependent on the version of the workflow that you want to run it might not be possible to re-build the Conda environment. Therefore, to guarantee reproducibility we create [container images](https://github.com/orgs/DKFZ-ODCF/packages) of the task environment. @@ -41,25 +23,47 @@ nextflow run main.nf \ In your cluster, you may not have access to Docker. In this situation you can use [Singularity](https://singularity.lbl.gov/), if it is installed in your cluster. Note that unfortunately, Nextflow will fail to convert the Docker image into a Singularity image, unless Docker is available. But you can get the Singularity image yourself: -1. Create a Singularity image from the public Docker container - ```bash - version=1.0.0 - repoDir=/path/to/nf-bam2fastq - - singularity build \ - "$repoDir/cache/singularity/nf-bam2fastq_$version.sif" \ - "docker://ghcr.io/dkfz-odcf/nf-bam2fastq:$version" - ``` - Note that the location and name of the Singularity image is configured in the `nextflow.config`. -3. Now, you can run the workflow with the "singularity" profile, e.g. on an LSF cluster: - ```bash - nextflow run /path/to/nf-bam2fastq/main.nf \ - -profile lsf,singularity \ - -ansi-log \ - --input=test/test1_paired.bam,test/test1_unpaired.bam \ - --outputDir=test_out \ - --sortFastqs=true - ``` +You can run the workflow with the "singularity" profile, e.g. on an LSF cluster: + +```bash +nextflow run $repoDir/main.nf \ + -profile lsf,singularity \ + --input=$repoDir/test/test1_paired.bam,$repoDir/test/test1_unpaired.bam \ + --outputDir=test_out \ + --sortFastqs=true +``` + +Nextflow will automatically pull the Docker image, convert it into a Singularity image, put it at `$repoDir/cache/singularity/ghcr.io-dkfz-odcf-nf-bam2fastq-$version.img`, and then run the workflow. + +> WARNING: Downloading the cached container is probably *not* concurrency-safe. If you run multiple workflows at the same time, all of them trying to cache the Singularity container, you will probably end up with a mess. In that case, download the container manually with following command to pull the container: +> ```bash +> version=1.0.0 +> repoDir=/path/to/nf-bam2fastq +> +> singularity build \ +> "$repoDir/cache/singularity/ghcr.io-dkfz-odcf-nf-bam2fastq-$version.img" \ +> "docker://ghcr.io/dkfz-odcf/nf-bam2fastq:$version" +> ``` + +## Quickstart with Conda + +> NOTE: Conda is a decent tool for building containers, although these containers tend to be rather big. However, we do *not* recommend you use Conda for reproducibly running workflows. The Conda solution proposed here really is mostly for development. We will not give support for this. + +We do not recommend Conda for running the workflow. It may happen that packages are not available in any channels anymore and that the environment is broken. For reproducible research, please use containers. + +Provided you have a working [Conda](https://docs.conda.io/en/latest/) installation, you can run the workflow with + +```bash +mkdir test_out/ +nextflow run main.nf \ + -profile local,conda \ + --input=/path/to/your.bam \ + --outputDir=test_out \ + --sortFastqs=false +``` + +For each BAM file in the comma-separated `--input` parameter, one directory with FASTQs is created in the `outputDir`. With the `local` profile the processing jobs will be executed locally. The `conda` profile will let Nextflow create a Conda environment from the `task-environment.yml` file. By default, the conda environment will be created in the source directory of the workflow (see [nextflow.config](https://github.com/DKFZ-ODCF/nf-bam2fastq/blob/master/nextflow.config)). + ## Remarks @@ -132,8 +136,8 @@ By default, the Conda environments of the jobs as well as the Singularity contai cd $workflowRepoDir # Refer to the nextflow.config for the name of the Singularity image. singularity build \ - cache/singularity/nf-bam2fastq_1.0.0.sif \ - docker://ghcr.io/dkfz-odcf/nf-bam2fastq:1.0.0 + cache/singularity/ghcr.io-dkfz-odcf-nf-bam2fastq-$version.img \ + docker://ghcr.io/dkfz-odcf/nf-bam2fastq:$version # Test your container test/test1.sh test-results/ singularity nextflowEnv/ @@ -189,6 +193,11 @@ This is an outline of the procedure to release the container to [Github Containe ## Release Notes +* 1.3.0 + * Minor: Let Nextflow automatically create the cached Singularity image. + > NOTE: The cached image name was changed to Nextflow's default name. If you want to prevent a re-conversion of the image, you may rename an existing image to `cache/singularity/ghcr.io-dkfz-odcf-nf-bam2fastq-$version.img`. + * Patch: Mention Conda only for development in `README.md`. + * 1.2.0 * Minor: Updated to miniconda3:4.10.3 base container, because the previous version (4.9.2) didn't build anymore. * Minor: Use `-env none` for "lsf" cluster profile. Local environment should not be copied. This probably caused problems with the old "dkfzModules" environment profile. diff --git a/main.nf b/main.nf index f45d92d..11a9f6f 100644 --- a/main.nf +++ b/main.nf @@ -162,10 +162,6 @@ String toSortMemoryString(MemoryUnit mem) { } /** The actual workflow */ -bamFiles_ch = Channel. - fromPath(params.input.split(',') as List, - checkIfExists: true) - Boolean compressBamToFastqOutput = params.sortFastqs ? params.compressIntermediateFastqs : true @@ -180,10 +176,10 @@ process bamToFastq { publishDir params.outputDir, enabled: !params.sortFastqs, mode: publishMode.toString() input: - file bamFile from bamFiles_ch + file bamFile output: - tuple file(bamFile), file("**/*.${fastqSuffix(compressBamToFastqOutput)}") into readsFiles_ch + tuple file(bamFile), file("**/*.${fastqSuffix(compressBamToFastqOutput)}") shell: """ @@ -199,29 +195,6 @@ process bamToFastq { } -// Create two channels of matched paired-end and unmatched or single-end reads, each of tuples of (bam, fastq). -readsFiles_ch.into { readsFilesA_ch; readsFilesB_ch } -pairedFastqs_ch = readsFilesA_ch.flatMap { - def (bam, fastqs) = it - fastqs.grep { it.getFileName() =~ /.+_R[12]\.fastq(?:\.[^.]*)?$/ }. - groupBy { fastq -> fastq.getFileName().toString().replaceFirst("_R[12].fastq(?:.gz)?\$", "") }. - collect { key, files -> - assert files.size() == 2 - files.sort() - [bam, files[0], files[1]] - } -} - - -// Unpaired FASTQs are unmatched or orphaned paired-reads (1 or 2) and singletons, i.e. unpaired reads. -unpairedFastqs_ch = readsFilesB_ch.flatMap { - def (bam, fastqs) = it - fastqs. - grep { it.getFileName() =~ /.+_(U[12]|S)\.fastq(?:\.[^.]*)?$/ }. - collect { [bam, it] } -} - - process nameSortUnpairedFastqs { cpus { params.sortThreads + (params.compressIntermediateFastqs ? params.compressorThreads : 0 ) } memory { (sortMemory + 100.MB) * params.sortThreads * 1.2 } @@ -235,15 +208,14 @@ process nameSortUnpairedFastqs { params.sortFastqs input: - tuple file(bam), file(fastq) from unpairedFastqs_ch + tuple file(bam), file(fastq) output: - tuple file(bam), file(sortedFastqFile) into sortedUnpairedFastqs_ch + tuple file(bam), file(sortedFastqFile) script: - bamFileName = bam.getFileName().toString() - outDir = "${bamFileName}_sorted_fastqs" - sortedFastqFile = sortedFastqFile(outDir, fastq, true) + outDir = "${bam.getFileName().toString()}_sorted_fastqs" as String + sortedFastqFile = sortedFastqFile(outDir, fastq.toRealPath(), true) """ mkdir -p "$outDir" compressedInputFastqs="$compressBamToFastqOutput" \ @@ -272,16 +244,15 @@ process nameSortPairedFastqs { params.sortFastqs input: - tuple file(bam), file(fastq1), file(fastq2) from pairedFastqs_ch + tuple file(bam), file(fastq1), file(fastq2) output: - tuple file(bam), file(sortedFastqFile1), file(sortedFastqFile2) into sortedPairedFastqs_ch + tuple file(bam), file(sortedFastqFile1), file(sortedFastqFile2) script: - bamFileName = bam.getFileName().toString() - outDir = "${bamFileName}_sorted_fastqs" - sortedFastqFile1 = sortedFastqFile(outDir, fastq1, true) - sortedFastqFile2 = sortedFastqFile(outDir, fastq2, true) + outDir = "${bam.getFileName().toString()}_sorted_fastqs" as String + sortedFastqFile1 = sortedFastqFile(outDir, fastq1.toRealPath(), true) + sortedFastqFile2 = sortedFastqFile(outDir, fastq2.toRealPath(), true) """ mkdir -p "$outDir" compressedInputFastqs="$compressBamToFastqOutput" \ @@ -298,6 +269,39 @@ process nameSortPairedFastqs { } +workflow { + + bamFiles_ch = Channel.fromPath(params.input.split(',') as List, checkIfExists: true) + readsFiles_ch = bamToFastq(bamFiles_ch) + + pairedFastqs_ch = readsFiles_ch.flatMap { + def (bam, fastqs) = it + fastqs.grep { + it.getFileName() =~ /.+_R[12]\.fastq(?:\.[^.]*)?$/ + }. + groupBy { fastq -> + fastq.getFileName().toString().replaceFirst("_R[12].fastq(?:.gz)?\$", "") + }. + collect { key, files -> + assert files.size() == 2 + files.sort() + [bam, files[0], files[1]] + } + } + nameSortPairedFastqs(pairedFastqs_ch) + + // Unpaired FASTQs are unmatched or orphaned paired-reads (1 or 2) and singletons, i.e. unpaired reads. + unpairedFastqs_ch = readsFiles_ch.flatMap { + def (bam, fastqs) = it + fastqs. + grep { it.getFileName() =~ /.+_(U[12]|S)\.fastq(?:\.[^.]*)?$/ }. + collect { [bam, it] } + } + nameSortUnpairedFastqs(unpairedFastqs_ch) + + +} + workflow.onComplete { println "Workflow run $workflow.runName completed at $workflow.complete with status " + diff --git a/nextflow.config b/nextflow.config index 0ca558d..2a6ec21 100644 --- a/nextflow.config +++ b/nextflow.config @@ -61,11 +61,15 @@ profiles { } singularity { - process.container = "nf-bam2fastq_${ext.containerVersion}.sif" + // Automatically pull the Docker image, and put it into the cache directory + process.container = "docker://ghcr.io/dkfz-odcf/nf-bam2fastq:${ext.containerVersion}" singularity.enabled = true singularity.cacheDir = "${projectDir}/cache/singularity" // The singularity containers are stored in the workflow-directory singularity.autoMounts = true + // Don't mount the home directory by default, because Bash may setup the environment from + // there thus breaking the environment encapsulation and reproducibility of the workflow. + singularity.runOptions = "--no-home" } lsf { diff --git a/test/test1.sh b/test/test1.sh index 1b560b3..6f629bc 100755 --- a/test/test1.sh +++ b/test/test1.sh @@ -10,7 +10,7 @@ set -ue set -o pipefail outDir="${1:?No outDir set}" -environmentProfile="${2:-conda}" +environmentProfile="${2:-singularity}" nextflowEnvironment="${3:-$outDir/nextflowEnv}" if [[ "$environmentProfile" == "mamba" ]]; then From 5ecc597cdfc66923dbfbef24c0095ca87f888f79 Mon Sep 17 00:00:00 2001 From: "Philip R. Kensche" Date: Wed, 6 Mar 2024 14:49:06 +0100 Subject: [PATCH 2/8] Added previous output as reference to the integration test. Signed-off-by: Philip R. 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binary patch literal 20 Ucmb2|=3ofOdXdV&%*+4-04k>fzyJUM literal 0 HcmV?d00001 diff --git a/test/test1.sh b/test/test1.sh index 6f629bc..066c3a8 100755 --- a/test/test1.sh +++ b/test/test1.sh @@ -78,18 +78,18 @@ nextflow run "$workflowDir/main.nf" \ -ansi-log \ -resume \ -work-dir "$outDir/work" \ - --input="$workflowDir/test/test1_paired.bam,$workflowDir/test/test1_unpaired.bam" \ + --input="$workflowDir/test/reference/test1_paired.bam,$workflowDir/test/reference/test1_unpaired.bam" \ --outputDir="$outDir" \ --sortFastqs=false \ --compressorThreads=0 \ --sortThreads=1 \ --sortMemory="100 MB" assertEqual \ - "$(readsInBam "$workflowDir/test/test1_paired.bam")" \ + "$(readsInBam "$workflowDir/test/reference/test1_paired.bam")" \ "$(readsInOutputDir "$outDir/test1_paired.bam_fastqs")" \ "Read number in unsorted output FASTQs on paired-end input bam" assertEqual \ - "$(readsInBam "$workflowDir/test/test1_unpaired.bam")" \ + "$(readsInBam "$workflowDir/test/reference/test1_unpaired.bam")" \ "$(readsInOutputDir "$outDir/test1_unpaired.bam_fastqs")" \ "Read number in unsorted output FASTQs on single-end input bam" @@ -98,19 +98,27 @@ nextflow run "$workflowDir/main.nf" \ -ansi-log \ -resume \ -work-dir "$outDir/work" \ - --input="$workflowDir/test/test1_paired.bam,$workflowDir/test/test1_unpaired.bam" \ + --input="$workflowDir/test/reference/test1_paired.bam,$workflowDir/test/reference/test1_unpaired.bam" \ --outputDir="$outDir" \ --sortFastqs=true \ --compressorThreads=0 \ --sortThreads=1 \ --sortMemory="100 MB" assertEqual \ - "$(readsInBam "$workflowDir/test/test1_paired.bam")" \ + "$(readsInBam "$workflowDir/test/reference/test1_paired.bam")" \ "$(readsInOutputDir "$outDir/test1_paired.bam_sorted_fastqs")" \ "Read number in sorted output FASTQs on paired-end input bam" assertEqual \ - "$(readsInBam "$workflowDir/test/test1_unpaired.bam")" \ + "$(readsInBam "$workflowDir/test/reference/test1_unpaired.bam")" \ "$(readsInOutputDir "$outDir/test1_unpaired.bam_sorted_fastqs")" \ "Read number in sorted output FASTQs on single-end input bam" +for ref in reference/test*/*; do + out="$outDir/$(echo "$ref" | sed "s/reference//")" + assertEqual \ + "$(zcat "$ref" | md5sum | cut -d' ' -f1)" \ + "$(zcat "$out" | md5sum | cut -d' ' -f1)" \ + "MD5 of $ref and $out" +done + testFinished From fed0e20157caa51c3839b47e5ae96e26144ece8d Mon Sep 17 00:00:00 2001 From: "Philip R. Kensche" Date: Wed, 6 Mar 2024 15:24:16 +0100 Subject: [PATCH 3/8] Typo fix in readme Signed-off-by: Philip R. Kensche --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 4b2b1a2..db9329b 100644 --- a/README.md +++ b/README.md @@ -197,6 +197,7 @@ This is an outline of the procedure to release the container to [Github Containe * Minor: Let Nextflow automatically create the cached Singularity image. > NOTE: The cached image name was changed to Nextflow's default name. If you want to prevent a re-conversion of the image, you may rename an existing image to `cache/singularity/ghcr.io-dkfz-odcf-nf-bam2fastq-$version.img`. * Patch: Mention Conda only for development in `README.md`. + * Patch: Test-script now implements a simple backwards-compatibility test by comparing against old result files. * 1.2.0 * Minor: Updated to miniconda3:4.10.3 base container, because the previous version (4.9.2) didn't build anymore. From d89566d9d30dad3b96502bfab54339d4eef5af3a Mon Sep 17 00:00:00 2001 From: "Philip R. Kensche" Date: Wed, 6 Mar 2024 15:37:32 +0100 Subject: [PATCH 4/8] Added example output directory. Signed-off-by: Philip R. Kensche --- README.md | 144 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 144 insertions(+) diff --git a/README.md b/README.md index db9329b..5631107 100644 --- a/README.md +++ b/README.md @@ -112,6 +112,150 @@ These files are all always produced, independent of whether your data is actuall Note that Nextflow creates the `work/` directory, the `.nextflow/` directory, and the `.nextflow.log*` files in the directory in which it is executed. +#### Example + +For instance, the output for the two test BAMs in the `test/reference/` directory would look as follows. Note that these files contain multiple read groups: + +```bash +$ samtools view -H | grep -P '^@RG' +@RG ID:run4_gerald_D1VCPACXX_4 LB:tumor_gms PL:ILLUMINA SM:sample_tumor_gms +@RG ID:run5_gerald_D1VCPACXX_5 LB:tumor_gms PL:ILLUMINA SM:sample_tumor_gms +@RG ID:run1_gerald_D1VCPACXX_1 LB:tumor_gms PL:ILLUMINA SM:sample_tumor_gms +@RG ID:run3_gerald_D1VCPACXX_3 LB:tumor_gms PL:ILLUMINA SM:sample_tumor_gms +@RG ID:run2_gerald_D1VCPACXX_2 LB:tumor_gms PL:ILLUMINA SM:sample_tumor_gms +``` + +Consequently, there will be a lot of output files: + +```bash +test1_paired.bam +test1_paired.bam_fastqs/ +├── default_R1.fastq.gz +├── default_R2.fastq.gz +├── default_S.fastq.gz +├── default_U1.fastq.gz +├── default_U2.fastq.gz +├── run1_gerald_D1VCPACXX_1_R1.fastq.gz +├── run1_gerald_D1VCPACXX_1_R2.fastq.gz +├── run1_gerald_D1VCPACXX_1_S.fastq.gz +├── run1_gerald_D1VCPACXX_1_U1.fastq.gz +├── run1_gerald_D1VCPACXX_1_U2.fastq.gz +├── run2_gerald_D1VCPACXX_2_R1.fastq.gz +├── run2_gerald_D1VCPACXX_2_R2.fastq.gz +├── run2_gerald_D1VCPACXX_2_S.fastq.gz +├── run2_gerald_D1VCPACXX_2_U1.fastq.gz +├── run2_gerald_D1VCPACXX_2_U2.fastq.gz +├── run3_gerald_D1VCPACXX_3_R1.fastq.gz +├── run3_gerald_D1VCPACXX_3_R2.fastq.gz +├── run3_gerald_D1VCPACXX_3_S.fastq.gz +├── run3_gerald_D1VCPACXX_3_U1.fastq.gz +├── run3_gerald_D1VCPACXX_3_U2.fastq.gz +├── run4_gerald_D1VCPACXX_4_R1.fastq.gz +├── run4_gerald_D1VCPACXX_4_R2.fastq.gz +├── run4_gerald_D1VCPACXX_4_S.fastq.gz +├── run4_gerald_D1VCPACXX_4_U1.fastq.gz +├── run4_gerald_D1VCPACXX_4_U2.fastq.gz +├── run5_gerald_D1VCPACXX_5_R1.fastq.gz +├── run5_gerald_D1VCPACXX_5_R2.fastq.gz +├── run5_gerald_D1VCPACXX_5_S.fastq.gz +├── run5_gerald_D1VCPACXX_5_U1.fastq.gz +└── run5_gerald_D1VCPACXX_5_U2.fastq.gz +test1_paired.bam_sorted_fastqs/ +├── default_R1.sorted.fastq.gz +├── default_R2.sorted.fastq.gz +├── default_S.sorted.fastq.gz +├── default_U1.sorted.fastq.gz +├── default_U2.sorted.fastq.gz +├── run1_gerald_D1VCPACXX_1_R1.sorted.fastq.gz +├── run1_gerald_D1VCPACXX_1_R2.sorted.fastq.gz +├── run1_gerald_D1VCPACXX_1_S.sorted.fastq.gz +├── run1_gerald_D1VCPACXX_1_U1.sorted.fastq.gz +├── run1_gerald_D1VCPACXX_1_U2.sorted.fastq.gz +├── run2_gerald_D1VCPACXX_2_R1.sorted.fastq.gz +├── run2_gerald_D1VCPACXX_2_R2.sorted.fastq.gz +├── run2_gerald_D1VCPACXX_2_S.sorted.fastq.gz +├── run2_gerald_D1VCPACXX_2_U1.sorted.fastq.gz +├── run2_gerald_D1VCPACXX_2_U2.sorted.fastq.gz +├── run3_gerald_D1VCPACXX_3_R1.sorted.fastq.gz +├── run3_gerald_D1VCPACXX_3_R2.sorted.fastq.gz +├── run3_gerald_D1VCPACXX_3_S.sorted.fastq.gz +├── run3_gerald_D1VCPACXX_3_U1.sorted.fastq.gz +├── run3_gerald_D1VCPACXX_3_U2.sorted.fastq.gz +├── run4_gerald_D1VCPACXX_4_R1.sorted.fastq.gz +├── run4_gerald_D1VCPACXX_4_R2.sorted.fastq.gz +├── run4_gerald_D1VCPACXX_4_S.sorted.fastq.gz +├── run4_gerald_D1VCPACXX_4_U1.sorted.fastq.gz +├── run4_gerald_D1VCPACXX_4_U2.sorted.fastq.gz +├── run5_gerald_D1VCPACXX_5_R1.sorted.fastq.gz +├── run5_gerald_D1VCPACXX_5_R2.sorted.fastq.gz +├── run5_gerald_D1VCPACXX_5_S.sorted.fastq.gz +├── run5_gerald_D1VCPACXX_5_U1.sorted.fastq.gz +└── run5_gerald_D1VCPACXX_5_U2.sorted.fastq.gz +test1_unpaired.bam +test1_unpaired.bam_fastqs/ +├── default_R1.fastq.gz +├── default_R2.fastq.gz +├── default_S.fastq.gz +├── default_U1.fastq.gz +├── default_U2.fastq.gz +├── run1_gerald_D1VCPACXX_1_R1.fastq.gz +├── run1_gerald_D1VCPACXX_1_R2.fastq.gz +├── run1_gerald_D1VCPACXX_1_S.fastq.gz +├── run1_gerald_D1VCPACXX_1_U1.fastq.gz +├── run1_gerald_D1VCPACXX_1_U2.fastq.gz +├── run2_gerald_D1VCPACXX_2_R1.fastq.gz +├── run2_gerald_D1VCPACXX_2_R2.fastq.gz +├── run2_gerald_D1VCPACXX_2_S.fastq.gz +├── run2_gerald_D1VCPACXX_2_U1.fastq.gz +├── run2_gerald_D1VCPACXX_2_U2.fastq.gz +├── run3_gerald_D1VCPACXX_3_R1.fastq.gz +├── run3_gerald_D1VCPACXX_3_R2.fastq.gz +├── run3_gerald_D1VCPACXX_3_S.fastq.gz +├── run3_gerald_D1VCPACXX_3_U1.fastq.gz +├── run3_gerald_D1VCPACXX_3_U2.fastq.gz +├── run4_gerald_D1VCPACXX_4_R1.fastq.gz +├── run4_gerald_D1VCPACXX_4_R2.fastq.gz +├── run4_gerald_D1VCPACXX_4_S.fastq.gz +├── run4_gerald_D1VCPACXX_4_U1.fastq.gz +├── run4_gerald_D1VCPACXX_4_U2.fastq.gz +├── run5_gerald_D1VCPACXX_5_R1.fastq.gz +├── run5_gerald_D1VCPACXX_5_R2.fastq.gz +├── run5_gerald_D1VCPACXX_5_S.fastq.gz +├── run5_gerald_D1VCPACXX_5_U1.fastq.gz +└── run5_gerald_D1VCPACXX_5_U2.fastq.gz +test1_unpaired.bam_sorted_fastqs/ +├── default_R1.sorted.fastq.gz +├── default_R2.sorted.fastq.gz +├── default_S.sorted.fastq.gz +├── default_U1.sorted.fastq.gz +├── default_U2.sorted.fastq.gz +├── run1_gerald_D1VCPACXX_1_R1.sorted.fastq.gz +├── run1_gerald_D1VCPACXX_1_R2.sorted.fastq.gz +├── run1_gerald_D1VCPACXX_1_S.sorted.fastq.gz +├── run1_gerald_D1VCPACXX_1_U1.sorted.fastq.gz +├── run1_gerald_D1VCPACXX_1_U2.sorted.fastq.gz +├── run2_gerald_D1VCPACXX_2_R1.sorted.fastq.gz +├── run2_gerald_D1VCPACXX_2_R2.sorted.fastq.gz +├── run2_gerald_D1VCPACXX_2_S.sorted.fastq.gz +├── run2_gerald_D1VCPACXX_2_U1.sorted.fastq.gz +├── run2_gerald_D1VCPACXX_2_U2.sorted.fastq.gz +├── run3_gerald_D1VCPACXX_3_R1.sorted.fastq.gz +├── run3_gerald_D1VCPACXX_3_R2.sorted.fastq.gz +├── run3_gerald_D1VCPACXX_3_S.sorted.fastq.gz +├── run3_gerald_D1VCPACXX_3_U1.sorted.fastq.gz +├── run3_gerald_D1VCPACXX_3_U2.sorted.fastq.gz +├── run4_gerald_D1VCPACXX_4_R1.sorted.fastq.gz +├── run4_gerald_D1VCPACXX_4_R2.sorted.fastq.gz +├── run4_gerald_D1VCPACXX_4_S.sorted.fastq.gz +├── run4_gerald_D1VCPACXX_4_U1.sorted.fastq.gz +├── run4_gerald_D1VCPACXX_4_U2.sorted.fastq.gz +├── run5_gerald_D1VCPACXX_5_R1.sorted.fastq.gz +├── run5_gerald_D1VCPACXX_5_R2.sorted.fastq.gz +├── run5_gerald_D1VCPACXX_5_S.sorted.fastq.gz +├── run5_gerald_D1VCPACXX_5_U1.sorted.fastq.gz +└── run5_gerald_D1VCPACXX_5_U2.sorted.fastq.gz +``` + ## Environment and Execution [Nextflow](https://www.nextflow.io/docs/latest/config.html#config-profiles)'s `-profile` parameter allows setting technical options for executing the workflow. You have already seen some of the profiles and that these can be combined. We conceptually separated the predefined profiles into two types -- those concerning the "environment" and those for selecting the "executor". From 1fc9ae064657c873e7bd091a46b00f243964efc9 Mon Sep 17 00:00:00 2001 From: "Philip R. Kensche" Date: Wed, 6 Mar 2024 17:39:42 +0100 Subject: [PATCH 5/8] Moved process.container config to multiple places, as it was not used with the old "lsf" profile, even if additionally the "singularity" profile was used. Signed-off-by: Philip R. Kensche --- nextflow.config | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/nextflow.config b/nextflow.config index 2a6ec21..59f738c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -19,50 +19,49 @@ manifest { // The workflow may refer to an older container version, e.g. if the container was not updated. ext.containerVersion = '1.0.0' +ext.containerUrl = "docker://ghcr.io/dkfz-odcf/nf-bam2fastq:${ext.containerVersion}" +ext.taskEnvYaml = "${projectDir}/task-environment.yml" profiles { + // It seems the `container` field is not used in the "lsf" profile, unless it is explicitly + // added as to the "lsf" block. I added it to all relevant "process" blocks. Whether it is + // going to be used, will depend on the `enabled` toggles in the `docker` and `singularity` + // profiles. + test { process { cpus = 1 memory = 1.GB + container = ext.containerUrl } } local { process { executor = 'local' + container = ext.containerUrl } } conda { conda.enabled = true conda.cacheDir = "${projectDir}/cache/conda" - process { - conda = "${projectDir}/task-environment.yml" - } } mamba { conda.enabled = true useMamba = true conda.cacheDir = "${projectDir}/cache/conda" - process { - conda = "${projectDir}/task-environment.yml" - } } docker { docker.enabled = true docker.runOptions='-u $(id -u):$(id -g)' - process { - container = "ghcr.io/dkfz-odcf/nf-bam2fastq:${ext.containerVersion}" - } } singularity { // Automatically pull the Docker image, and put it into the cache directory - process.container = "docker://ghcr.io/dkfz-odcf/nf-bam2fastq:${ext.containerVersion}" singularity.enabled = true singularity.cacheDir = "${projectDir}/cache/singularity" // The singularity containers are stored in the workflow-directory @@ -76,6 +75,7 @@ profiles { process { executor = 'lsf' clusterOptions = '-env none' + container = ext.containerUrl } executor { // scratch = '$SCRATCHDIR/$LSB_JOBID' From 76032e07f4a981be1960128e0005e2305ab9898d Mon Sep 17 00:00:00 2001 From: "Philip R. Kensche" Date: Thu, 7 Mar 2024 09:53:30 +0100 Subject: [PATCH 6/8] Updated Nextflow for the tests. Found a way to combine process options from different profiles. Signed-off-by: Philip R. Kensche --- nextflow.config | 42 +++++++++++++++++------------------------- test-environment.yml | 2 +- 2 files changed, 18 insertions(+), 26 deletions(-) diff --git a/nextflow.config b/nextflow.config index 59f738c..888ebf6 100644 --- a/nextflow.config +++ b/nextflow.config @@ -19,29 +19,23 @@ manifest { // The workflow may refer to an older container version, e.g. if the container was not updated. ext.containerVersion = '1.0.0' -ext.containerUrl = "docker://ghcr.io/dkfz-odcf/nf-bam2fastq:${ext.containerVersion}" +ext.containerUrl = "ghcr.io/dkfz-odcf/nf-bam2fastq:${ext.containerVersion}" ext.taskEnvYaml = "${projectDir}/task-environment.yml" profiles { - // It seems the `container` field is not used in the "lsf" profile, unless it is explicitly - // added as to the "lsf" block. I added it to all relevant "process" blocks. Whether it is - // going to be used, will depend on the `enabled` toggles in the `docker` and `singularity` - // profiles. + // Note, that here we don't use `process { ... }` but `executor { ... }` blocks, as these + // would override the settings from other profiles. The current settings allow to combine + // profiles, e.g. test,lsf,singularity, to run the workflow with test resources on LSF using + // Singularity containers. test { - process { - cpus = 1 - memory = 1.GB - container = ext.containerUrl - } + process.cpus = 1 + process.memory = 1.GB } local { - process { - executor = 'local' - container = ext.containerUrl - } + process.executor = 'local' } conda { @@ -51,13 +45,14 @@ profiles { mamba { conda.enabled = true - useMamba = true + conda.useMamba = true conda.cacheDir = "${projectDir}/cache/conda" } docker { docker.enabled = true docker.runOptions='-u $(id -u):$(id -g)' + process.container = ext.containerUrl } singularity { @@ -69,19 +64,16 @@ profiles { // Don't mount the home directory by default, because Bash may setup the environment from // there thus breaking the environment encapsulation and reproducibility of the workflow. singularity.runOptions = "--no-home" + process.container = "docker://${ext.containerUrl}" } lsf { - process { - executor = 'lsf' - clusterOptions = '-env none' - container = ext.containerUrl - } - executor { - // scratch = '$SCRATCHDIR/$LSB_JOBID' - perTaskReserve = false - perJobMemLimit = true - } + process.executor = 'lsf' + process.clusterOptions = '-env none' + + // executor.scratch = '$SCRATCHDIR/$LSB_JOBID' + executor.perTaskReserve = false + executor.perJobMemLimit = true } } diff --git a/test-environment.yml b/test-environment.yml index ae3e642..7897f12 100755 --- a/test-environment.yml +++ b/test-environment.yml @@ -7,6 +7,6 @@ dependencies: - mamba - bash=5.0.018 - samtools=1.11 - - nextflow=22.10.1 + - nextflow=23.10.1 - gradle=7.4.2 - openjdk=11.0.15 From 1c7cef5e9743cbe1fc839547f01c2a7fdd86fbf3 Mon Sep 17 00:00:00 2001 From: "Philip R. Kensche" Date: Fri, 8 Mar 2024 16:00:39 +0100 Subject: [PATCH 7/8] Updated Dockerfile and Singularity.def. Moved test/run.sh to integration-testsd/run.sh. Signed-off-by: Philip R. Kensche --- .circleci/config.yml | 8 +-- .dockerignore | 7 ++- .gitignore | 2 + Dockerfile | 53 ------------------ README.md | 48 +++++++++------- container-specs/Dockerfile | 36 ++++++++++++ container-specs/Singularity.def | 15 +++++ .../reference/test1_paired.bam | Bin .../default_R1.fastq.gz | Bin .../default_R2.fastq.gz | Bin .../default_S.fastq.gz | Bin .../default_U1.fastq.gz | Bin .../default_U2.fastq.gz | Bin .../run1_gerald_D1VCPACXX_1_R1.fastq.gz | Bin .../run1_gerald_D1VCPACXX_1_R2.fastq.gz | Bin .../run1_gerald_D1VCPACXX_1_S.fastq.gz | Bin .../run1_gerald_D1VCPACXX_1_U1.fastq.gz | Bin .../run1_gerald_D1VCPACXX_1_U2.fastq.gz | Bin .../run2_gerald_D1VCPACXX_2_R1.fastq.gz | Bin .../run2_gerald_D1VCPACXX_2_R2.fastq.gz | Bin .../run2_gerald_D1VCPACXX_2_S.fastq.gz | Bin .../run2_gerald_D1VCPACXX_2_U1.fastq.gz | Bin .../run2_gerald_D1VCPACXX_2_U2.fastq.gz | Bin .../run3_gerald_D1VCPACXX_3_R1.fastq.gz | Bin .../run3_gerald_D1VCPACXX_3_R2.fastq.gz | Bin .../run3_gerald_D1VCPACXX_3_S.fastq.gz | Bin .../run3_gerald_D1VCPACXX_3_U1.fastq.gz | Bin .../run3_gerald_D1VCPACXX_3_U2.fastq.gz | Bin .../run4_gerald_D1VCPACXX_4_R1.fastq.gz | Bin .../run4_gerald_D1VCPACXX_4_R2.fastq.gz | Bin .../run4_gerald_D1VCPACXX_4_S.fastq.gz | Bin .../run4_gerald_D1VCPACXX_4_U1.fastq.gz | Bin .../run4_gerald_D1VCPACXX_4_U2.fastq.gz | Bin .../run5_gerald_D1VCPACXX_5_R1.fastq.gz | Bin .../run5_gerald_D1VCPACXX_5_R2.fastq.gz | Bin .../run5_gerald_D1VCPACXX_5_S.fastq.gz | Bin .../run5_gerald_D1VCPACXX_5_U1.fastq.gz | Bin .../run5_gerald_D1VCPACXX_5_U2.fastq.gz | Bin .../default_R1.sorted.fastq.gz | Bin .../default_R2.sorted.fastq.gz | Bin .../default_S.sorted.fastq.gz | Bin .../default_U1.sorted.fastq.gz | Bin .../default_U2.sorted.fastq.gz | Bin ...run1_gerald_D1VCPACXX_1_R1.sorted.fastq.gz | Bin ...run1_gerald_D1VCPACXX_1_R2.sorted.fastq.gz | Bin .../run1_gerald_D1VCPACXX_1_S.sorted.fastq.gz | Bin ...run1_gerald_D1VCPACXX_1_U1.sorted.fastq.gz | Bin ...run1_gerald_D1VCPACXX_1_U2.sorted.fastq.gz | Bin ...run2_gerald_D1VCPACXX_2_R1.sorted.fastq.gz | Bin ...run2_gerald_D1VCPACXX_2_R2.sorted.fastq.gz | Bin .../run2_gerald_D1VCPACXX_2_S.sorted.fastq.gz | Bin ...run2_gerald_D1VCPACXX_2_U1.sorted.fastq.gz | Bin ...run2_gerald_D1VCPACXX_2_U2.sorted.fastq.gz | Bin ...run3_gerald_D1VCPACXX_3_R1.sorted.fastq.gz | Bin ...run3_gerald_D1VCPACXX_3_R2.sorted.fastq.gz | Bin .../run3_gerald_D1VCPACXX_3_S.sorted.fastq.gz | Bin ...run3_gerald_D1VCPACXX_3_U1.sorted.fastq.gz | Bin ...run3_gerald_D1VCPACXX_3_U2.sorted.fastq.gz | Bin ...run4_gerald_D1VCPACXX_4_R1.sorted.fastq.gz | Bin ...run4_gerald_D1VCPACXX_4_R2.sorted.fastq.gz | Bin .../run4_gerald_D1VCPACXX_4_S.sorted.fastq.gz | Bin ...run4_gerald_D1VCPACXX_4_U1.sorted.fastq.gz | Bin ...run4_gerald_D1VCPACXX_4_U2.sorted.fastq.gz | Bin ...run5_gerald_D1VCPACXX_5_R1.sorted.fastq.gz | Bin ...run5_gerald_D1VCPACXX_5_R2.sorted.fastq.gz | Bin .../run5_gerald_D1VCPACXX_5_S.sorted.fastq.gz | Bin ...run5_gerald_D1VCPACXX_5_U1.sorted.fastq.gz | Bin ...run5_gerald_D1VCPACXX_5_U2.sorted.fastq.gz | Bin .../reference/test1_unpaired.bam | Bin .../default_R1.fastq.gz | Bin .../default_R2.fastq.gz | Bin .../default_S.fastq.gz | Bin .../default_U1.fastq.gz | Bin .../default_U2.fastq.gz | Bin .../run1_gerald_D1VCPACXX_1_R1.fastq.gz | Bin .../run1_gerald_D1VCPACXX_1_R2.fastq.gz | Bin .../run1_gerald_D1VCPACXX_1_S.fastq.gz | Bin .../run1_gerald_D1VCPACXX_1_U1.fastq.gz | Bin .../run1_gerald_D1VCPACXX_1_U2.fastq.gz | Bin .../run2_gerald_D1VCPACXX_2_R1.fastq.gz | Bin .../run2_gerald_D1VCPACXX_2_R2.fastq.gz | Bin .../run2_gerald_D1VCPACXX_2_S.fastq.gz | Bin .../run2_gerald_D1VCPACXX_2_U1.fastq.gz | Bin .../run2_gerald_D1VCPACXX_2_U2.fastq.gz | Bin .../run3_gerald_D1VCPACXX_3_R1.fastq.gz | Bin .../run3_gerald_D1VCPACXX_3_R2.fastq.gz | Bin .../run3_gerald_D1VCPACXX_3_S.fastq.gz | Bin .../run3_gerald_D1VCPACXX_3_U1.fastq.gz | Bin .../run3_gerald_D1VCPACXX_3_U2.fastq.gz | Bin .../run4_gerald_D1VCPACXX_4_R1.fastq.gz | Bin .../run4_gerald_D1VCPACXX_4_R2.fastq.gz | Bin .../run4_gerald_D1VCPACXX_4_S.fastq.gz | Bin .../run4_gerald_D1VCPACXX_4_U1.fastq.gz | Bin .../run4_gerald_D1VCPACXX_4_U2.fastq.gz | Bin .../run5_gerald_D1VCPACXX_5_R1.fastq.gz | Bin .../run5_gerald_D1VCPACXX_5_R2.fastq.gz | Bin .../run5_gerald_D1VCPACXX_5_S.fastq.gz | Bin .../run5_gerald_D1VCPACXX_5_U1.fastq.gz | Bin .../run5_gerald_D1VCPACXX_5_U2.fastq.gz | Bin .../default_R1.sorted.fastq.gz | Bin .../default_R2.sorted.fastq.gz | Bin .../default_S.sorted.fastq.gz | Bin .../default_U1.sorted.fastq.gz | Bin .../default_U2.sorted.fastq.gz | Bin ...run1_gerald_D1VCPACXX_1_R1.sorted.fastq.gz | Bin ...run1_gerald_D1VCPACXX_1_R2.sorted.fastq.gz | Bin .../run1_gerald_D1VCPACXX_1_S.sorted.fastq.gz | Bin ...run1_gerald_D1VCPACXX_1_U1.sorted.fastq.gz | Bin ...run1_gerald_D1VCPACXX_1_U2.sorted.fastq.gz | Bin ...run2_gerald_D1VCPACXX_2_R1.sorted.fastq.gz | Bin ...run2_gerald_D1VCPACXX_2_R2.sorted.fastq.gz | Bin .../run2_gerald_D1VCPACXX_2_S.sorted.fastq.gz | Bin ...run2_gerald_D1VCPACXX_2_U1.sorted.fastq.gz | Bin ...run2_gerald_D1VCPACXX_2_U2.sorted.fastq.gz | Bin ...run3_gerald_D1VCPACXX_3_R1.sorted.fastq.gz | Bin ...run3_gerald_D1VCPACXX_3_R2.sorted.fastq.gz | Bin .../run3_gerald_D1VCPACXX_3_S.sorted.fastq.gz | Bin ...run3_gerald_D1VCPACXX_3_U1.sorted.fastq.gz | Bin ...run3_gerald_D1VCPACXX_3_U2.sorted.fastq.gz | Bin ...run4_gerald_D1VCPACXX_4_R1.sorted.fastq.gz | Bin ...run4_gerald_D1VCPACXX_4_R2.sorted.fastq.gz | Bin .../run4_gerald_D1VCPACXX_4_S.sorted.fastq.gz | Bin ...run4_gerald_D1VCPACXX_4_U1.sorted.fastq.gz | Bin ...run4_gerald_D1VCPACXX_4_U2.sorted.fastq.gz | Bin ...run5_gerald_D1VCPACXX_5_R1.sorted.fastq.gz | Bin ...run5_gerald_D1VCPACXX_5_R2.sorted.fastq.gz | Bin .../run5_gerald_D1VCPACXX_5_S.sorted.fastq.gz | Bin ...run5_gerald_D1VCPACXX_5_U1.sorted.fastq.gz | Bin ...run5_gerald_D1VCPACXX_5_U2.sorted.fastq.gz | Bin test/test1.sh => integration-tests/run.sh | 17 +++--- nextflow.config | 11 ++-- nf-bam2fastq.iml | 3 +- task-environment.yml | 1 + test-environment.yml | 2 +- 134 files changed, 107 insertions(+), 96 deletions(-) delete mode 100644 Dockerfile create mode 100644 container-specs/Dockerfile create mode 100644 container-specs/Singularity.def rename {test => integration-tests}/reference/test1_paired.bam (100%) rename {test => integration-tests}/reference/test1_paired.bam_fastqs/default_R1.fastq.gz (100%) rename {test => integration-tests}/reference/test1_paired.bam_fastqs/default_R2.fastq.gz (100%) rename {test => integration-tests}/reference/test1_paired.bam_fastqs/default_S.fastq.gz (100%) rename {test => integration-tests}/reference/test1_paired.bam_fastqs/default_U1.fastq.gz (100%) rename {test => integration-tests}/reference/test1_paired.bam_fastqs/default_U2.fastq.gz (100%) rename {test => integration-tests}/reference/test1_paired.bam_fastqs/run1_gerald_D1VCPACXX_1_R1.fastq.gz (100%) rename {test => 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keys: - - v1-nextflow-env-{{ .Branch }}-{{ checksum "test-environment.yml" }} + - v1-nextflow-env-{{ .Branch }}-{{ checksum "tests-environment.yml" }} - restore_cache: keys: - v1-job-env-{{ .Branch }}-{{ checksum "task-environment.yml" }} - run: name: "run integration tests" - command: "test/test1.sh test-results/ mamba nextflowEnv/" + command: "integration-tests/run.sh tests-results/ mamba nextflowEnv/" - save_cache: - key: v1-nextflow-env-{{ .Branch }}-{{ checksum "test-environment.yml" }} + key: v1-nextflow-env-{{ .Branch }}-{{ checksum "tests-environment.yml" }} paths: - nextflowEnv/ - save_cache: @@ -38,4 +38,4 @@ jobs: workflows: test-workflow: jobs: - - integration-test + - integration-tests diff --git a/.dockerignore b/.dockerignore index 5b8b7a5..89eaadd 100644 --- a/.dockerignore +++ b/.dockerignore @@ -9,5 +9,10 @@ work .circleci cache .git +.github .gitignore -nextflowEnv +*Env/ +integration-tests/ +.run/ +*.log +*Env/ \ No newline at end of file diff --git a/.gitignore b/.gitignore index 9e609fe..cc9e385 100644 --- a/.gitignore +++ b/.gitignore @@ -14,3 +14,5 @@ cache/singularity/* *~ *.sif .git +.run/ +*Env/ diff --git a/Dockerfile b/Dockerfile deleted file mode 100644 index 32178c5..0000000 --- a/Dockerfile +++ /dev/null @@ -1,53 +0,0 @@ -FROM continuumio/miniconda3:4.10.3 - -LABEL maintainer="Philip R. Kensche " - -# Capitalized versions for many tools. Minuscle version at least for apt. -ARG HTTP_PROXY="" -ARG http_proxy="$HTTP_PROXY" -ARG HTTPS_PROXY="" -ARG https_proxy="$HTTPS_PROXY" -ARG NO_PROXY="" -ARG no_proxy="$NO_PROXY" - -# Setup base conda container with bash as default shell. -SHELL ["/bin/bash", "-c"] -RUN conda init bash - -# Add nf-bam2fastq requirements. -LABEL org.opencontainers.image.source="https://github.com/dkfz-odcf/nf-bam2fastq" -COPY task-environment.yml ./ -RUN conda config --set proxy_servers.http "$HTTP_PROXY" && \ - conda config --set proxy_servers.https "$HTTPS_PROXY" && \ - conda env create -n nf-bam2fastq -f task-environment.yml && \ - source activate nf-bam2fastq && \ - conda clean --all -f -y - -# ps is needed by Nextflow for collecting runtime information from the container -RUN apt update && \ - apt-get install -y procps && \ - rm -rf /var/lib/apt/lists/* && \ - apt clean - -# For login Bash /etc/profile and ~/.profile is sourced. /etc/profile sources /etc/bash.bashrc. -# For non-login, interactive Bash /etc/bash.bashrc is sourced directly. -# For non-login, non-interactive Bash. We set BASH_ENV/ENV to /etc/bash.bashrc -# NOTE: ~/.bashrc could not be used, because when using it, ~/ is /root/. -# Therefore /etc/bash.bashrc is used to use conda for all user IDs. -# NOTE: Conda should be fully available in non-login, interactive shell. Conda itself creates -# /etc/profile.d/conda.sh. The code that `conda init bash` writes to ~/.bashrc is moved -# to /etc/bash.bashrc and reads the /etc/profile.d/conda.sh. -ENV BASH_ENV /etc/container.bashrc -ENV ENV /etc/container.bashrc - -RUN grep "managed by 'conda init'" -A 100 ~/.bashrc >> /etc/container.bashrc && \ - rm ~/.bashrc && \ - echo -e '\ -set +u\n\ -source activate nf-bam2fastq\n\ -set -u\n\' >> /etc/container.bashrc && \ - echo "source /etc/profile" > ~/.profile && \ - cp ~/.profile /.profile && \ - echo "source /etc/container.bashrc" >> /etc/bash.bashrc - -ENTRYPOINT ["bash", "-i", "-c"] diff --git a/README.md b/README.md index 5631107..ec6b724 100644 --- a/README.md +++ b/README.md @@ -14,7 +14,7 @@ For instance, if you want to run the workflow locally with Docker you can do e.g nextflow run main.nf \ -profile local,docker \ -ansi-log \ - --input=test/test1_paired.bam,test/test1_unpaired.bam \ + --input=integration-tests/test1_paired.bam,integration-tests/test1_unpaired.bam \ --outputDir=test_out \ --sortFastqs=true ``` @@ -28,21 +28,21 @@ You can run the workflow with the "singularity" profile, e.g. on an LSF cluster: ```bash nextflow run $repoDir/main.nf \ -profile lsf,singularity \ - --input=$repoDir/test/test1_paired.bam,$repoDir/test/test1_unpaired.bam \ + --input=$repoDir/integration-tests/test1_paired.bam,$repoDir/integration-tests/test1_unpaired.bam \ --outputDir=test_out \ --sortFastqs=true ``` -Nextflow will automatically pull the Docker image, convert it into a Singularity image, put it at `$repoDir/cache/singularity/ghcr.io-dkfz-odcf-nf-bam2fastq-$version.img`, and then run the workflow. +Nextflow will automatically pull the Docker image, convert it into a Singularity image, put it at `$repoDir/cache/singularity/ghcr.io-dkfz-odcf-nf-bam2fastq-$containerVersion.img`, and then run the workflow. > WARNING: Downloading the cached container is probably *not* concurrency-safe. If you run multiple workflows at the same time, all of them trying to cache the Singularity container, you will probably end up with a mess. In that case, download the container manually with following command to pull the container: > ```bash -> version=1.0.0 +> containerVersion=1.3.0 > repoDir=/path/to/nf-bam2fastq > > singularity build \ -> "$repoDir/cache/singularity/ghcr.io-dkfz-odcf-nf-bam2fastq-$version.img" \ -> "docker://ghcr.io/dkfz-odcf/nf-bam2fastq:$version" +> "$repoDir/cache/singularity/ghcr.io-dkfz-odcf-nf-bam2fastq-$containerVersion.img" \ +> "docker://ghcr.io/dkfz-odcf/nf-bam2fastq:$containerVersion" > ``` ## Quickstart with Conda @@ -114,7 +114,7 @@ Note that Nextflow creates the `work/` directory, the `.nextflow/` directory, an #### Example -For instance, the output for the two test BAMs in the `test/reference/` directory would look as follows. Note that these files contain multiple read groups: +For instance, the output for the two test BAMs in the `integration-tests/reference/` directory would look as follows. Note that these files contain multiple read groups: ```bash $ samtools view -H | grep -P '^@RG' @@ -280,11 +280,11 @@ By default, the Conda environments of the jobs as well as the Singularity contai cd $workflowRepoDir # Refer to the nextflow.config for the name of the Singularity image. singularity build \ - cache/singularity/ghcr.io-dkfz-odcf-nf-bam2fastq-$version.img \ - docker://ghcr.io/dkfz-odcf/nf-bam2fastq:$version + cache/singularity/ghcr.io-dkfz-odcf-nf-bam2fastq-$containerVersion.img \ + container-specs/Singularity.def # Test your container -test/test1.sh test-results/ singularity nextflowEnv/ +integration-tests/run.sh tests-results/ singularity nextflowEnv/ ``` This is suited for either a user-specific installation or for a centralized installation for which the environments should be shared for all users. Please refer to the `nextflow.config` or the `NXF_*_CACHEDIR` environment variables to change this default (see [here](https://www.nextflow.io/docs/latest/config.html#environment-variables). @@ -296,7 +296,7 @@ Make sure your users have read and execute permissions on the directories and re The integration tests can be run with ```bash -test/test1.sh test-results/ $profile +integration-tests/run.sh tests-results/ $profile ``` This will create a test Conda environment in `test-results/nextflowEnv` and then run the tests. For the tests themselves you can use a local Conda environment or a Docker container, dependent on whether you set `$profile` to "conda" or "docker", respectively. These integration tests are also run in Travis CI. @@ -313,37 +313,43 @@ This is an outline of the procedure to release the container to [Github Containe 1. Set the version that you want to release as variable. For the later commands you can set the Bash variable ```bash - versionTag=1.2.0 + containerVersion=1.3.0 ``` 2. Build the container. - ```bash + ```bash docker \ build \ - -t ghcr.io/dkfz-odcf/nf-bam2fastq:$versionTag \ + -t ghcr.io/dkfz-odcf/nf-bam2fastq:$containerVersion \ --build-arg HTTP_PROXY=$HTTP_PROXY \ --build-arg HTTPS_PROXY=$HTTPS_PROXY \ + -f container-specs/Dockerfile \ ./ ``` -3. Edit the version-tag for the docker container in the "docker"-profile in the `nextflow.config` to match `$versionTag`. +3. Edit the version-tag for the docker container in the "docker"-profile in the `nextflow.config` to match `$containerVersion`. 4. Run the integration test with the new container ```bash - test/test1.sh docker-test docker + integration-tests/run.sh docker-tests docker ``` 5. If the test succeeds, push the container to Github container registry. Set the CR_PAT variable to your personal access token (PAT): ```bash echo $CR_PAT | docker login ghcr.io -u vinjana --password-stdin - docker image push ghcr.io/dkfz-odcf/nf-bam2fastq:$versionTag + docker image push ghcr.io/dkfz-odcf/nf-bam2fastq:$containerVersion ``` ## Release Notes -* 1.3.0 +* 1.3.0 (March, 2024) * Minor: Let Nextflow automatically create the cached Singularity image. - > NOTE: The cached image name was changed to Nextflow's default name. If you want to prevent a re-conversion of the image, you may rename an existing image to `cache/singularity/ghcr.io-dkfz-odcf-nf-bam2fastq-$version.img`. - * Patch: Mention Conda only for development in `README.md`. + > NOTE: The cached image name was changed to Nextflow's default name. + * Patch: Reuse to the simpler Dockerfile that is also used in the [nf-seq-qc](https://gitlab.com/one-touch-pipeline/workflows/nf-seq-qc) and [nf-seq-convert](https://gitlab.com/one-touch-pipeline/workflows/nf-seq-convert) workflows. + * Patch: Bumped Dockerfile base image to miniconda3:4.12.0. + * Patch: Bumped minimum Nextflow to 23.10.1. Version 22 uses `singularity exec`, while 23 uses `singularity run`, which impacts process isolation. + * Patch: Added a `Singularity.def`, in case the automatic conversion by Nextflow does not work. + * Patch: Mention Conda only for development in `README.md`. Otherwise, it should not be used. * Patch: Test-script now implements a simple backwards-compatibility test by comparing against old result files. + * Patch: Renamed `test/test1.sh` to `integration-tests/run.sh`. -* 1.2.0 +* 1.2.0 (May, 2023) * Minor: Updated to miniconda3:4.10.3 base container, because the previous version (4.9.2) didn't build anymore. * Minor: Use `-env none` for "lsf" cluster profile. Local environment should not be copied. This probably caused problems with the old "dkfzModules" environment profile. * Patch: Require Nextflow >= 22.07.1, which fixes an LSF memory request bug. Added options for per-job memory requests to "lsf" profile in `nextflow.config`. diff --git a/container-specs/Dockerfile b/container-specs/Dockerfile new file mode 100644 index 0000000..1a4cffc --- /dev/null +++ b/container-specs/Dockerfile @@ -0,0 +1,36 @@ +# SPDX-FileCopyrightText: 2024 The OTP authors +# +# SPDX-License-Identifier: MIT + +FROM continuumio/miniconda3:4.12.0 + +LABEL maintainer="Philip R. Kensche " + +# Capitalized versions for many tools. Minuscle version at least for apt. +ARG HTTP_PROXY="" +ARG http_proxy="$HTTP_PROXY" +ARG HTTPS_PROXY="" +ARG https_proxy="$HTTPS_PROXY" +ARG NO_PROXY="" +ARG no_proxy="$NO_PROXY" + +# Setup base conda container with bash as default shell. +SHELL ["/bin/bash", "-c"] +RUN conda init bash + +# Now, the stuff that needs to be rebuild for every workflow/container. +# The envName can be reused in later layers, and in a Singularity.def. +ENV envName="nf-bam2fastq" +LABEL org.opencontainers.image.source="https://ghcr.io/dkfz-odcf/$envName" + +COPY task-environment.yml ./ + +RUN conda config --set proxy_servers.http "$HTTP_PROXY" && \ + conda config --set proxy_servers.https "$HTTPS_PROXY" && \ + conda env create -n "$envName" -f task-environment.yml && \ + source activate "$envName" && \ + conda clean --all -f -y + +# Use -p path instead of -n name to activate the environment. Otherwise, Conda will fail with +# NoWritableEnvsDirError. +ENTRYPOINT ["conda", "run", "--no-capture-output", "-p", "/opt/conda/envs/$envName"] diff --git a/container-specs/Singularity.def b/container-specs/Singularity.def new file mode 100644 index 0000000..e00fe29 --- /dev/null +++ b/container-specs/Singularity.def @@ -0,0 +1,15 @@ +# SPDX-FileCopyrightText: 2023 The OTP authors +# +# SPDX-License-Identifier: MIT + +# This file is needed for the conversion of the Docker image into a Singularity image that +# can be executed with `singularity exec`, like Nextflow does it. `singularity exec` does *not* +# invoke the runscript, but the environment initialization in the Dockerfile is done via the +# ENTRYPOINT and that is converted into the Singularity runscript. +# +# Note that the docker-daemon bootstrap allows to do this with locally tagged images. +Bootstrap: docker-daemon +From: ghcr.io/dkfz-odcf/nf-bam2fastq:1.3.0 + +%environment + source activate "$envName" diff --git a/test/reference/test1_paired.bam b/integration-tests/reference/test1_paired.bam similarity index 100% rename from test/reference/test1_paired.bam rename to integration-tests/reference/test1_paired.bam diff --git a/test/reference/test1_paired.bam_fastqs/default_R1.fastq.gz b/integration-tests/reference/test1_paired.bam_fastqs/default_R1.fastq.gz similarity index 100% rename from test/reference/test1_paired.bam_fastqs/default_R1.fastq.gz rename to integration-tests/reference/test1_paired.bam_fastqs/default_R1.fastq.gz diff --git a/test/reference/test1_paired.bam_fastqs/default_R2.fastq.gz b/integration-tests/reference/test1_paired.bam_fastqs/default_R2.fastq.gz similarity index 100% rename from test/reference/test1_paired.bam_fastqs/default_R2.fastq.gz rename to integration-tests/reference/test1_paired.bam_fastqs/default_R2.fastq.gz diff --git a/test/reference/test1_paired.bam_fastqs/default_S.fastq.gz b/integration-tests/reference/test1_paired.bam_fastqs/default_S.fastq.gz similarity 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diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_R1.sorted.fastq.gz b/integration-tests/reference/test1_unpaired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_R1.sorted.fastq.gz similarity index 100% rename from test/reference/test1_unpaired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_R1.sorted.fastq.gz rename to integration-tests/reference/test1_unpaired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_R1.sorted.fastq.gz diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_R2.sorted.fastq.gz b/integration-tests/reference/test1_unpaired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_R2.sorted.fastq.gz similarity index 100% rename from test/reference/test1_unpaired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_R2.sorted.fastq.gz rename to integration-tests/reference/test1_unpaired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_R2.sorted.fastq.gz diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_S.sorted.fastq.gz b/integration-tests/reference/test1_unpaired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_S.sorted.fastq.gz similarity index 100% rename from test/reference/test1_unpaired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_S.sorted.fastq.gz rename to integration-tests/reference/test1_unpaired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_S.sorted.fastq.gz diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_U1.sorted.fastq.gz b/integration-tests/reference/test1_unpaired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_U1.sorted.fastq.gz similarity index 100% rename from test/reference/test1_unpaired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_U1.sorted.fastq.gz rename to integration-tests/reference/test1_unpaired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_U1.sorted.fastq.gz diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_U2.sorted.fastq.gz b/integration-tests/reference/test1_unpaired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_U2.sorted.fastq.gz 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test/reference/test1_unpaired.bam_sorted_fastqs/run3_gerald_D1VCPACXX_3_R2.sorted.fastq.gz rename to integration-tests/reference/test1_unpaired.bam_sorted_fastqs/run3_gerald_D1VCPACXX_3_R2.sorted.fastq.gz diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run3_gerald_D1VCPACXX_3_S.sorted.fastq.gz b/integration-tests/reference/test1_unpaired.bam_sorted_fastqs/run3_gerald_D1VCPACXX_3_S.sorted.fastq.gz similarity index 100% rename from test/reference/test1_unpaired.bam_sorted_fastqs/run3_gerald_D1VCPACXX_3_S.sorted.fastq.gz rename to integration-tests/reference/test1_unpaired.bam_sorted_fastqs/run3_gerald_D1VCPACXX_3_S.sorted.fastq.gz diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run3_gerald_D1VCPACXX_3_U1.sorted.fastq.gz b/integration-tests/reference/test1_unpaired.bam_sorted_fastqs/run3_gerald_D1VCPACXX_3_U1.sorted.fastq.gz similarity index 100% rename from test/reference/test1_unpaired.bam_sorted_fastqs/run3_gerald_D1VCPACXX_3_U1.sorted.fastq.gz rename to 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diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run4_gerald_D1VCPACXX_4_U1.sorted.fastq.gz b/integration-tests/reference/test1_unpaired.bam_sorted_fastqs/run4_gerald_D1VCPACXX_4_U1.sorted.fastq.gz similarity index 100% rename from test/reference/test1_unpaired.bam_sorted_fastqs/run4_gerald_D1VCPACXX_4_U1.sorted.fastq.gz rename to integration-tests/reference/test1_unpaired.bam_sorted_fastqs/run4_gerald_D1VCPACXX_4_U1.sorted.fastq.gz diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run4_gerald_D1VCPACXX_4_U2.sorted.fastq.gz b/integration-tests/reference/test1_unpaired.bam_sorted_fastqs/run4_gerald_D1VCPACXX_4_U2.sorted.fastq.gz similarity index 100% rename from test/reference/test1_unpaired.bam_sorted_fastqs/run4_gerald_D1VCPACXX_4_U2.sorted.fastq.gz rename to integration-tests/reference/test1_unpaired.bam_sorted_fastqs/run4_gerald_D1VCPACXX_4_U2.sorted.fastq.gz diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_R1.sorted.fastq.gz b/integration-tests/reference/test1_unpaired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_R1.sorted.fastq.gz similarity index 100% rename from test/reference/test1_unpaired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_R1.sorted.fastq.gz rename to integration-tests/reference/test1_unpaired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_R1.sorted.fastq.gz diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_R2.sorted.fastq.gz b/integration-tests/reference/test1_unpaired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_R2.sorted.fastq.gz similarity index 100% rename from test/reference/test1_unpaired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_R2.sorted.fastq.gz rename to integration-tests/reference/test1_unpaired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_R2.sorted.fastq.gz diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_S.sorted.fastq.gz b/integration-tests/reference/test1_unpaired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_S.sorted.fastq.gz similarity index 100% rename from test/reference/test1_unpaired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_S.sorted.fastq.gz rename to integration-tests/reference/test1_unpaired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_S.sorted.fastq.gz diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_U1.sorted.fastq.gz b/integration-tests/reference/test1_unpaired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_U1.sorted.fastq.gz similarity index 100% rename from test/reference/test1_unpaired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_U1.sorted.fastq.gz rename to integration-tests/reference/test1_unpaired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_U1.sorted.fastq.gz diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_U2.sorted.fastq.gz b/integration-tests/reference/test1_unpaired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_U2.sorted.fastq.gz similarity index 100% rename from test/reference/test1_unpaired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_U2.sorted.fastq.gz rename to integration-tests/reference/test1_unpaired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_U2.sorted.fastq.gz diff --git a/test/test1.sh b/integration-tests/run.sh similarity index 81% rename from test/test1.sh rename to integration-tests/run.sh index 066c3a8..107fc00 100755 --- a/test/test1.sh +++ b/integration-tests/run.sh @@ -1,6 +1,6 @@ #!/bin/bash # -# Copyright (c) 2022 DKFZ. +# Copyright (c) 2024 DKFZ. # # Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/nf-bam2fastq/blob/master/LICENSE.txt). # @@ -13,7 +13,7 @@ outDir="${1:?No outDir set}" environmentProfile="${2:-singularity}" nextflowEnvironment="${3:-$outDir/nextflowEnv}" -if [[ "$environmentProfile" == "mamba" ]]; then +if command -v mamba; then condaBinary=mamba else condaBinary=conda @@ -71,6 +71,7 @@ set -ue # Keep memory footprint small export NXF_OPTS="-Xmx128m" +export NXF_SINGULARITY_RUN_COMMAND=run # Run the tests. nextflow run "$workflowDir/main.nf" \ @@ -78,18 +79,18 @@ nextflow run "$workflowDir/main.nf" \ -ansi-log \ -resume \ -work-dir "$outDir/work" \ - --input="$workflowDir/test/reference/test1_paired.bam,$workflowDir/test/reference/test1_unpaired.bam" \ + --input="$workflowDir/integration-tests/reference/test1_paired.bam,$workflowDir/integration-tests/reference/test1_unpaired.bam" \ --outputDir="$outDir" \ --sortFastqs=false \ --compressorThreads=0 \ --sortThreads=1 \ --sortMemory="100 MB" assertEqual \ - "$(readsInBam "$workflowDir/test/reference/test1_paired.bam")" \ + "$(readsInBam "$workflowDir/integration-tests/reference/test1_paired.bam")" \ "$(readsInOutputDir "$outDir/test1_paired.bam_fastqs")" \ "Read number in unsorted output FASTQs on paired-end input bam" assertEqual \ - "$(readsInBam "$workflowDir/test/reference/test1_unpaired.bam")" \ + "$(readsInBam "$workflowDir/integration-tests/reference/test1_unpaired.bam")" \ "$(readsInOutputDir "$outDir/test1_unpaired.bam_fastqs")" \ "Read number in unsorted output FASTQs on single-end input bam" @@ -98,18 +99,18 @@ nextflow run "$workflowDir/main.nf" \ -ansi-log \ -resume \ -work-dir "$outDir/work" \ - --input="$workflowDir/test/reference/test1_paired.bam,$workflowDir/test/reference/test1_unpaired.bam" \ + --input="$workflowDir/integration-tests/reference/test1_paired.bam,$workflowDir/integration-tests/reference/test1_unpaired.bam" \ --outputDir="$outDir" \ --sortFastqs=true \ --compressorThreads=0 \ --sortThreads=1 \ --sortMemory="100 MB" assertEqual \ - "$(readsInBam "$workflowDir/test/reference/test1_paired.bam")" \ + "$(readsInBam "$workflowDir/integration-tests/reference/test1_paired.bam")" \ "$(readsInOutputDir "$outDir/test1_paired.bam_sorted_fastqs")" \ "Read number in sorted output FASTQs on paired-end input bam" assertEqual \ - "$(readsInBam "$workflowDir/test/reference/test1_unpaired.bam")" \ + "$(readsInBam "$workflowDir/integration-tests/reference/test1_unpaired.bam")" \ "$(readsInOutputDir "$outDir/test1_unpaired.bam_sorted_fastqs")" \ "Read number in sorted output FASTQs on single-end input bam" diff --git a/nextflow.config b/nextflow.config index 888ebf6..3e0cb80 100644 --- a/nextflow.config +++ b/nextflow.config @@ -14,11 +14,11 @@ manifest { mainScript = 'main.nf' version = '1.2.0' author = 'Philip Reiner Kensche' - nextflowVersion = '>= 22.07.1' + nextflowVersion = '>= 23.10.1' } // The workflow may refer to an older container version, e.g. if the container was not updated. -ext.containerVersion = '1.0.0' +ext.containerVersion = '1.3.0' ext.containerUrl = "ghcr.io/dkfz-odcf/nf-bam2fastq:${ext.containerVersion}" ext.taskEnvYaml = "${projectDir}/task-environment.yml" @@ -26,7 +26,7 @@ profiles { // Note, that here we don't use `process { ... }` but `executor { ... }` blocks, as these // would override the settings from other profiles. The current settings allow to combine - // profiles, e.g. test,lsf,singularity, to run the workflow with test resources on LSF using + // profiles, e.g. tests,lsf,singularity, to run the workflow with tests resources on LSF using // Singularity containers. test { @@ -61,10 +61,7 @@ profiles { singularity.cacheDir = "${projectDir}/cache/singularity" // The singularity containers are stored in the workflow-directory singularity.autoMounts = true - // Don't mount the home directory by default, because Bash may setup the environment from - // there thus breaking the environment encapsulation and reproducibility of the workflow. - singularity.runOptions = "--no-home" - process.container = "docker://${ext.containerUrl}" + process.container = "docker-daemon://${ext.containerUrl}" } lsf { diff --git a/nf-bam2fastq.iml b/nf-bam2fastq.iml index ad12601..90cacad 100644 --- a/nf-bam2fastq.iml +++ b/nf-bam2fastq.iml @@ -10,14 +10,15 @@ - + + \ No newline at end of file diff --git a/task-environment.yml b/task-environment.yml index 73f8f63..9628cae 100755 --- a/task-environment.yml +++ b/task-environment.yml @@ -4,6 +4,7 @@ channels: - bioconda - defaults dependencies: + - procps-ng - _libgcc_mutex=0.1=conda_forge - _openmp_mutex=4.5=1_gnu - bash=5.0.018=h0a1914f_0 diff --git a/test-environment.yml b/test-environment.yml index 7897f12..2e7570c 100755 --- a/test-environment.yml +++ b/test-environment.yml @@ -1,4 +1,4 @@ -name: test-environment +name: tests-environment channels: - conda-forge - bioconda From fb45af80b7cdf436e8f38833541ceaeb1f6a6bcf Mon Sep 17 00:00:00 2001 From: "Philip R. Kensche" Date: Fri, 8 Mar 2024 17:05:37 +0100 Subject: [PATCH 8/8] Changed order of integration-test/run.sh parameters. Signed-off-by: Philip R. Kensche --- .circleci/config.yml | 2 +- README.md | 10 +++++----- integration-tests/run.sh | 10 ++++++---- 3 files changed, 12 insertions(+), 10 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 7861362..1e8d627 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -23,7 +23,7 @@ jobs: - v1-job-env-{{ .Branch }}-{{ checksum "task-environment.yml" }} - run: name: "run integration tests" - command: "integration-tests/run.sh tests-results/ mamba nextflowEnv/" + command: "integration-tests/run.sh mamba tests-results/ nextflowEnv/" - save_cache: key: v1-nextflow-env-{{ .Branch }}-{{ checksum "tests-environment.yml" }} paths: diff --git a/README.md b/README.md index ec6b724..74a65af 100644 --- a/README.md +++ b/README.md @@ -284,7 +284,7 @@ singularity build \ container-specs/Singularity.def # Test your container -integration-tests/run.sh tests-results/ singularity nextflowEnv/ +integration-tests/run.sh singularity test-results/ nextflowEnv/ ``` This is suited for either a user-specific installation or for a centralized installation for which the environments should be shared for all users. Please refer to the `nextflow.config` or the `NXF_*_CACHEDIR` environment variables to change this default (see [here](https://www.nextflow.io/docs/latest/config.html#environment-variables). @@ -296,10 +296,10 @@ Make sure your users have read and execute permissions on the directories and re The integration tests can be run with ```bash -integration-tests/run.sh tests-results/ $profile +integration-tests/run.sh $profile test-results/ ``` -This will create a test Conda environment in `test-results/nextflowEnv` and then run the tests. For the tests themselves you can use a local Conda environment or a Docker container, dependent on whether you set `$profile` to "conda" or "docker", respectively. These integration tests are also run in Travis CI. +This will create a test Conda environment in `./nextflowEnv` and then run the tests. For the tests themselves you can use a local Conda environment or a Docker container, dependent on whether you set `$profile` to "conda" or "docker", respectively. These integration tests are also run in Travis CI. ### Continuous Delivery @@ -328,7 +328,7 @@ This is an outline of the procedure to release the container to [Github Containe 3. Edit the version-tag for the docker container in the "docker"-profile in the `nextflow.config` to match `$containerVersion`. 4. Run the integration test with the new container ```bash - integration-tests/run.sh docker-tests docker + integration-tests/run.sh docker docker-test-results/ ``` 5. If the test succeeds, push the container to Github container registry. Set the CR_PAT variable to your personal access token (PAT): ```bash @@ -347,7 +347,7 @@ This is an outline of the procedure to release the container to [Github Containe * Patch: Added a `Singularity.def`, in case the automatic conversion by Nextflow does not work. * Patch: Mention Conda only for development in `README.md`. Otherwise, it should not be used. * Patch: Test-script now implements a simple backwards-compatibility test by comparing against old result files. - * Patch: Renamed `test/test1.sh` to `integration-tests/run.sh`. + * Patch: Renamed `test/test1.sh` to `integration-tests/run.sh`. Changed order of parameters. * 1.2.0 (May, 2023) * Minor: Updated to miniconda3:4.10.3 base container, because the previous version (4.9.2) didn't build anymore. diff --git a/integration-tests/run.sh b/integration-tests/run.sh index 107fc00..4582a61 100755 --- a/integration-tests/run.sh +++ b/integration-tests/run.sh @@ -9,9 +9,11 @@ set -x set -ue set -o pipefail -outDir="${1:?No outDir set}" -environmentProfile="${2:-singularity}" -nextflowEnvironment="${3:-$outDir/nextflowEnv}" +testsDir="$(readlink -f "$(dirname "${BASH_SOURCE[0]}")")" + +environmentProfile="${1:-singularity}" +outDir="${2:?No outDir set}" +nextflowEnvironment="${3:-$testsDir/nextflowEnv}" if command -v mamba; then condaBinary=mamba @@ -19,7 +21,7 @@ else condaBinary=conda fi -workflowDir="$(readlink -f "$(dirname "${BASH_SOURCE[0]}")/..")" +workflowDir="$testsDir/.." readsInBam() { local bamFile="${1:?No BAM file given}"