Merge pull request #51 from DKFZ-ODCF/lsf-env-none-fix

Lsf env none fix

.circleci/config.yml

@@ -6,7 +6,7 @@ version: 2.1
 # See: https://circleci.com/docs/2.0/configuration-reference/#jobs
 jobs:
   integration-test:
-    resource_class: small
+    resource_class: medium
     # Specify the execution environment. You can specify an image from Dockerhub or use one of our Convenience Images from CircleCI's Developer Hub.
     # See: https://circleci.com/docs/2.0/configuration-reference/#docker-machine-macos-windows-executor
     docker:

.gitignore

@@ -13,5 +13,4 @@ cache/singularity/*
 *.html.*
 *~
 *.sif
-.circleci
 .git

Dockerfile

@@ -4,9 +4,9 @@ LABEL maintainer="Philip R. Kensche <p.kensche@dkfz.de>"
 
 # Capitalized versions for many tools. Minuscle version at least for apt.
 ARG HTTP_PROXY=""
-ARG http_proxy=""
+ARG http_proxy="$HTTP_PROXY"
 ARG HTTPS_PROXY=""
-ARG https_proxy=""
+ARG https_proxy="$HTTPS_PROXY"
 ARG NO_PROXY=""
 ARG no_proxy="$NO_PROXY"
 
@@ -32,7 +32,7 @@ RUN apt update && \
 # 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 because ~/ is /root/.
+# 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
@@ -45,14 +45,7 @@ RUN grep "managed by 'conda init'" -A 100 ~/.bashrc >> /etc/container.bashrc &&
     echo -e '\
 set +u\n\
 source activate nf-bam2fastq\n\
-set -u\n\
-export SAMTOOLS_BINARY=samtools\n\
-export PICARD_BINARY=picard\n\
-export JAVA_BINARY=java\n\
-export MBUFFER_BINARY=mbuffer\n\
-export CHECKSUM_BINARY=md5sum\n\
-export PERL_BINARY=perl\n\
-export BIOBAMBAM_BAM2FASTQ_BINARY=bamtofastq\n' >> /etc/container.bashrc && \
+set -u\n\' >> /etc/container.bashrc && \
     echo "source /etc/profile" > ~/.profile && \
     cp ~/.profile /.profile && \
     echo "source /etc/container.bashrc" >> /etc/bash.bashrc

README.md

@@ -6,6 +6,8 @@ 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
@@ -124,14 +126,14 @@ Please refer to the [Nextflow documentation](https://www.nextflow.io/docs/latest
 
 ### Location of Environments
 
-By default the Conda environments of the jobs as well as the Singularity containers are stored in subdirectories of the `cache/` subdirectory of the workflows installation directory (a.k.a `projectDir` by Nextflow). E.g. to use the Singularity container you can install the container as follows
+By default, the Conda environments of the jobs as well as the Singularity containers are stored in subdirectories of the `cache/` subdirectory of the workflows installation directory (a.k.a `projectDir` by Nextflow). E.g. to use the Singularity container you can install the container as follows
 
 ```bash
 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-daemon://ghcr.io/dkfz-odcf/nf-bam2fastq:latest
+  docker://ghcr.io/dkfz-odcf/nf-bam2fastq:1.0.0
   
 # Test your container
 test/test1.sh test-results/ singularity nextflowEnv/
@@ -151,6 +153,10 @@ test/test1.sh test-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.
 
+### Continuous Delivery
+
+For all commits with a tag that follows the pattern `\d+\.\d+\.\d+` the job containers are automatically pushed to [Github Container Registry](https://github.com/orgs/DKFZ-ODCF/packages) of the "ODCF" organization. Version tags should only be added to commits on the `master` branch, although currently no automatic rule enforces this.
+
 ### Manual container release
 
 The container includes a Conda installation and is pretty big. It should only be released if its content is actually changed. For instance, it would be perfectly fine to have a workflow version 1.6.5 but still refer to an old container for 1.2.7.
@@ -159,7 +165,7 @@ 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=1.0.0
+   versionTag=1.2.0
    ```
 2. Build the container.
   ```bash
@@ -170,32 +176,31 @@ This is an outline of the procedure to release the container to [Github Containe
       --build-arg HTTPS_PROXY=$HTTPS_PROXY \
       ./
    ```
-3. Edit the version-tag for the docker container in the "docker"-profile in the nextflow.config to match `$versionTag`. 
+3. Edit the version-tag for the docker container in the "docker"-profile in the `nextflow.config` to match `$versionTag`.
 4. Run the integration test with the new container
    ```bash
-   test/test1.sh docker-test docker-test/test-environment docker
+   test/test1.sh docker-test 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
    ```
 
-### Continuous Delivery
-
-For all commits with a tag that follows the pattern `\d+\.\d+\.\d+` the job containers are automatically pushed to [Github Container Registry](https://github.com/orgs/DKFZ-ODCF/packages) of the "ODCF" organization. Version tags should only be added to commits on the `master` branch, although currently no automatic rule enforces this.
-
 ## Release Notes
 
-* upcoming
+* 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.
+  * 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`.
+  * Patch: Remove unnecessary `*_BINARY` variables in scripts. Binaries are fixed by Conda/containers.
+  * Patch: Needed to explicitly set `conda.enabled = True` with newer Nextflow
 
 * 1.1.0 (February, 2022)
   * Minor: Added `--publishMode` option to allow user to select the [Nextflow publish mode](https://www.nextflow.io/docs/latest/process.html#publishdir). Default: `rellink`. Note that the former default was `symlink`, but as this change is considered negligible we classified the change as "minor".
   * Minor: Removed `dkfzModules` profile. Didn't work well and was originally only for development. Please use 'conda', 'singularity' or 'docker'. The container-based environments provide the best reproducibility.
   * Patch: Switched from Travis to CircleCI for continuous integration.
 
-
 * 1.0.1 (October 14., 2021)
   * Patch: Fix memory calculation as exponential backoff
   * Patch: Job names now contain workflow name and job/task hash. Run name seems currently not possible to include there (due to a possible bug in Nextflow).

bin/bam2Fastq.sh

@@ -21,6 +21,7 @@ printInfo
 set -o pipefail
 set -uvex
 
+
 getFastqSuffix() {
     if [[ "$compressFastqs" == true ]]; then
         echo "fastq.gz"
@@ -66,7 +67,7 @@ processPairedEndWithReadGroups() {
     ##
     mkdir -p "$outputDir"
     local tempFile="$outputDir/$(basename "$bamFile").bamtofastq_tmp"
-    $BIOBAMBAM_BAM2FASTQ_BINARY \
+    bamtofastq \
         filename="$bamFile" \
         T="$tempFile" \
         outputperreadgroup=1 \
@@ -94,7 +95,7 @@ ensureAllFiles() {
 
 
 main() {
-    "$SAMTOOLS_BINARY" quickcheck "$bamFile"
+    samtools quickcheck "$bamFile"
 
     outputDir=${outputDir:-$(basename "$bamFile")"_fastqs"}
 

bin/workflowLib.sh

@@ -39,7 +39,7 @@ mbuf() {
   local bufferSize="$1"
   shift
   assertNonEmpty "$bufferSize" "No buffer size defined for mbuf()" || return $?
-  "$MBUFFER_BINARY" -m "$bufferSize" -q -l /dev/null $@
+  mbuffer -m "$bufferSize" -q -l /dev/null $@
 }
 
 lockFileName() {
@@ -84,7 +84,7 @@ assertNoDefaultReadGroup() {
 
 getReadGroups() {
   local bamFile="${1:?No BAM file given}"
-  declare -a groups=( $($SAMTOOLS_BINARY view -H "$bamFile" \
+  declare -a groups=( $(samtools view -H "$bamFile" \
     | grep -P '^@RG\s' \
     | perl -ne 's/^\@RG\s+ID:(\S+).*?$/$1/; print' \
     2>/dev/null) )
@@ -261,7 +261,7 @@ fastqLinearize() {
 }
 
 fastqDelinearize() {
-  "$PERL_BINARY" -aF\\t -lne '$F[0] =~ s/^(\S+?)(?:\/\d)?(?:\s+.*)?$/$1/o; print join("\n", @F)'
+  perl -aF\\t -lne '$F[0] =~ s/^(\S+?)(?:\/\d)?(?:\s+.*)?$/$1/o; print join("\n", @F)'
 }
 
 sortLinearizedFastqStream() {

nextflow.config

@@ -1,5 +1,5 @@
 /**
- *  Copyright (c) 2021 DKFZ.
+ *  Copyright (c) 2022 DKFZ.
  *
  *  Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/nf-bam2fastq/blob/master/LICENSE.txt).
  *
@@ -8,16 +8,17 @@
  *  Configuration for the DKFZ-ODCF/nf-bam2fastq Nextflow workflow.
  */
 
-nextflowVersion = '>= 20.04.1.5335'
-
 manifest {
     homePage = 'https://github.com/DKFZ-ODCF/nf-bam2fastq'
     description = 'BAM-to-FASTQ conversion and FASTQ-sorting workflow'
     mainScript = 'main.nf'
-    version = '1.1.0'
+    version = '1.2.0'
     author = 'Philip Reiner Kensche'
+    nextflowVersion = '>= 22.07.1'
 }
 
+// The workflow may refer to an older container version, e.g. if the container was not updated.
+ext.containerVersion = '1.0.0'
 
 profiles {
 
@@ -35,52 +36,32 @@ profiles {
     }
 
     conda {
-
+        conda.enabled = true
+        conda.cacheDir = "${projectDir}/cache/conda"
         process {
             conda = "${projectDir}/task-environment.yml"
-
-            beforeScript = """
-            export SAMTOOLS_BINARY=samtools
-            export PICARD_BINARY=picard
-            export JAVA_BINARY=java
-            export MBUFFER_BINARY=mbuffer
-            export CHECKSUM_BINARY=md5sum
-            export PERL_BINARY=perl
-            export BIOBAMBAM_BAM2FASTQ_BINARY=bamtofastq
-            """
         }
-        conda.cacheDir = "${projectDir}/cache/conda"
     }
 
     mamba {
+        conda.enabled = true
         useMamba = true
-
+        conda.cacheDir = "${projectDir}/cache/conda"
         process {
             conda = "${projectDir}/task-environment.yml"
-
-            beforeScript = """
-            export SAMTOOLS_BINARY=samtools
-            export PICARD_BINARY=picard
-            export JAVA_BINARY=java
-            export MBUFFER_BINARY=mbuffer
-            export CHECKSUM_BINARY=md5sum
-            export PERL_BINARY=perl
-            export BIOBAMBAM_BAM2FASTQ_BINARY=bamtofastq
-            """
         }
-        conda.cacheDir = "${projectDir}/cache/conda"
     }
 
     docker {
         docker.enabled = true
         docker.runOptions='-u $(id -u):$(id -g)'
         process {
-          container = 'ghcr.io/dkfz-odcf/nf-bam2fastq:1.0.0'
+          container = "ghcr.io/dkfz-odcf/nf-bam2fastq:${ext.containerVersion}"
         }
     }
 
     singularity {
-        process.container = 'nf-bam2fastq_1.0.0.sif'
+        process.container = "nf-bam2fastq_${ext.containerVersion}.sif"
         singularity.enabled = true
         singularity.cacheDir = "${projectDir}/cache/singularity"
         // The singularity containers are stored in the workflow-directory
@@ -90,6 +71,12 @@ profiles {
     lsf {
         process {
             executor = 'lsf'
+            clusterOptions = '-env none'
+        }
+        executor {
+            // scratch = '$SCRATCHDIR/$LSB_JOBID'
+            perTaskReserve = false
+            perJobMemLimit = true
         }
     }
 

nf-bam2fastq.iml

@@ -12,6 +12,8 @@
       <excludeFolder url="file://$MODULE_DIR$/cache/conda/nf-bam2fastq-3e98300235b5aed9f3835e00669fb59f" />
       <excludeFolder url="file://$MODULE_DIR$/test/output-all" />
       <excludeFolder url="file://$MODULE_DIR$/.nextflow" />
+      <excludeFolder url="file://$MODULE_DIR$/cache" />
+      <excludeFolder url="file://$MODULE_DIR$/nextflowEnv" />
     </content>
     <orderEntry type="inheritedJdk" />
     <orderEntry type="sourceFolder" forTests="false" />

task-environment.yml

@@ -1,13 +1,51 @@
-name: nf-bam2fastq 
+name: nf-bam2fastq
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
-  - bash=5.0.018
-  - biobambam=2.0.179
-  - mbuffer=20160228
-  - perl=5.22.2.1
-  - pigz=2.3.4
-  - python=3.6
-  - samtools=1.11
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=1_gnu
+  - bash=5.0.018=h0a1914f_0
+  - biobambam=2.0.179=h7d875b9_1
+  - boost-cpp=1.74.0=h312852a_4
+  - bzip2=1.0.8=h7f98852_4
+  - c-ares=1.17.1=h7f98852_1
+  - ca-certificates=2021.5.30=ha878542_0
+  - certifi=2021.5.30=py36h5fab9bb_0
+  - curl=7.77.0=hea6ffbf_0
+  - htslib=1.11=hd3b49d5_2
+  - icu=68.1=h58526e2_0
+  - krb5=1.19.1=hcc1bbae_0
+  - ld_impl_linux-64=2.35.1=hea4e1c9_2
+  - libcurl=7.77.0=h2574ce0_0
+  - libdeflate=1.7=h7f98852_5
+  - libedit=3.1.20191231=he28a2e2_2
+  - libev=4.33=h516909a_1
+  - libffi=3.3=h58526e2_2
+  - libgcc-ng=9.3.0=h2828fa1_19
+  - libgomp=9.3.0=h2828fa1_19
+  - libmaus2=2.0.777=h6eb57d2_0
+  - libnghttp2=1.43.0=h812cca2_0
+  - libssh2=1.9.0=ha56f1ee_6
+  - libstdcxx-ng=9.3.0=h6de172a_19
+  - lz4-c=1.9.3=h9c3ff4c_0
+  - mbuffer=20160228=h779adbc_3
+  - ncurses=6.2=h58526e2_4
+  - openssl=1.1.1k=h7f98852_0
+  - perl=5.22.2.1=0
+  - pigz=2.3.4=hed695b0_1
+  - pip=21.1.2=pyhd8ed1ab_0
+  - python=3.6.13=hffdb5ce_0_cpython
+  - python_abi=3.6=1_cp36m
+  - readline=8.1=h46c0cb4_0
+  - samtools=1.11=h6270b1f_0
+  - setuptools=49.6.0=py36h5fab9bb_3
+  - snappy=1.1.8=he1b5a44_3
+  - sqlite=3.35.5=h74cdb3f_0
+  - staden_io_lib=1.14.14=h7c09d56_1
+  - tk=8.6.10=h21135ba_1
+  - wheel=0.36.2=pyhd3deb0d_0
+  - xz=5.2.5=h516909a_1
+  - zlib=1.2.11=h516909a_1010
+  - zstd=1.5.0=ha95c52a_0

test-environment.yml

@@ -4,6 +4,9 @@ channels:
   - bioconda
   - defaults
 dependencies:
+  - mamba
   - bash=5.0.018
   - samtools=1.11
-  - nextflow=20.10.0
+  - nextflow=22.10.1
+  - gradle=7.4.2
+  - openjdk=11.0.15