update container setup

src/rsem/rsem_calculate_expression/config.vsh.yaml

@@ -31,6 +31,7 @@ argument_groups:
     multiple: true
   - name: "--index"
     type: file
+    must_exist: false
     description: RSEM index.  
   - name: "--extra_args"
     type: string
@@ -81,29 +82,59 @@ resources:
 test_resources:
   - type: bash_script
     path: test.sh
-  - path: /testData/minimal_test/input_fastq/SRR6357070_1.fastq.gz
-  - path: /testData/minimal_test/input_fastq/SRR6357070_2.fastq.gz
-  - path: /testData/minimal_test/reference/rsem.tar.gz
-
-# TODO: Install bowtie/bowtie2 
+  - path: test_data
+
 engines:
   - type: docker
     image: ubuntu:22.04
     setup:
-      - type: docker
-        run: |
-          apt-get update && \
-          apt-get install -y --no-install-recommends build-essential gcc g++ make wget zlib1g-dev unzip && \
-          apt-get clean && \
-          wget --no-check-certificate https://github.com/alexdobin/STAR/archive/refs/tags/2.7.11a.zip && \
-          unzip 2.7.11a.zip && \
-          cp STAR-2.7.11a/bin/Linux_x86_64_static/STAR /usr/local/bin  && \
-          cd && \
-          wget --no-check-certificate https://github.com/deweylab/RSEM/archive/refs/tags/v1.3.3.zip && \
-          unzip v1.3.3.zip && \
-          cd RSEM-1.3.3 && \
-          make && \
-          make install
+    - type: apt
+      packages: 
+        - build-essential 
+        - gcc 
+        - g++ 
+        - make 
+        - wget 
+        - zlib1g-dev 
+        - unzip 
+        - xxd 
+        - perl 
+        - r-base
+        - bowtie2
+        - python3-pip 
+        - git
+    - type: docker
+      env: 
+        - STAR_VERSION=2.7.11b
+        - RSEM_VERSION=1.3.3
+        - TZ=Europe/Brussels
+      run: |
+        ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone && \
+        cd /tmp && \
+        wget --no-check-certificate https://github.com/alexdobin/STAR/archive/refs/tags/${STAR_VERSION}.zip && \
+        unzip ${STAR_VERSION}.zip && \
+        cd STAR-${STAR_VERSION}/source && \
+        make STARstatic CXXFLAGS_SIMD=-std=c++11 && \
+        cp STAR /usr/local/bin && \
+        cd /tmp && \
+        wget --no-check-certificate https://github.com/deweylab/RSEM/archive/refs/tags/v${RSEM_VERSION}.zip && \
+        unzip v${RSEM_VERSION}.zip && \
+        cd RSEM-${RSEM_VERSION} && \
+        make && \
+        make install && \
+        rm -rf /tmp/STAR-${STAR_VERSION} /tmp/${STAR_VERSION}.zip && \
+        rm -rf /tmp/RSEM-${RSEM_VERSION} /tmp/v${RSEM_VERSION}.zip && \
+        cd && \
+        apt-get clean && \
+        echo 'export PATH=$PATH:/usr/local/bin' >> /etc/profile && \
+        echo 'export PATH=$PATH:/usr/local/bin' >> ~/.bashrc && \
+        /bin/bash -c "source /etc/profile && source ~/.bashrc && echo $PATH && which STAR"
+
+    - type: docker
+      run: |
+        echo "RSEM: `rsem-calculate-expression --version | sed -e 's/Current version: RSEM v//g'`" > /var/software_versions.txt && \
+        echo "STAR: `STAR --version | sed -e 's/STAR_//g'`" >> /var/software_versions.txt >> /var/software_versions.txt
+
 runners:
   - type: executable
   - type: nextflow

src/rsem/rsem_calculate_expression/script.sh

@@ -1,5 +1,8 @@
 #!/bin/bash
 
+## VIASH START
+## VIASH END
+
 set -eo pipefail
 
 function clean_up {
@@ -12,30 +15,20 @@ tmpdir=$(mktemp -d "$meta_temp_dir/$meta_functionality_name-XXXXXXXX")
 if [ $par_strandedness == 'forward' ]; then
     strandedness='--strandedness forward'
 elif [ $par_strandedness == 'reverse' ]; then
-    strandedness='--strandedness reverse'
+    strandedness="--strandedness reverse"
 else
     strandedness=''
 fi
 
-IFS="," read -ra input <<< $par_input
+IFS=";" read -ra input <<< $par_input
 
-INDEX=$(find -L $meta_resources_dir/ -name "*.grp" | sed 's/\.grp$//')
+INDEX=$(find -L "${meta_resources_dir}/${par_index}/" -name "*.grp" | sed 's/\.grp$//')
 
 rsem-calculate-expression \
-    ${meta_cpus:+--num-theads $meta_cpus} \
     $strandedness \
     ${par_paired:+--paired-end} \
     $par_extra_args \
     ${input[*]} \
     $INDEX \
     $par_id
-
-# Version
-text="${meta_functionality_name}:
-    rsem: $(rsem-calculate-expression --version | sed -e 's/Current version: RSEM v//g')"
-if [ -e "$par_versions" ]; then
-    echo "$text" >> "$par_versions"
-    mv "$par_versions" "$par_updated_versions"
-else
-    echo "$text" > "$par_updated_versions"
-fi     
+

src/rsem/rsem_calculate_expression/test.sh

@@ -1,19 +1,20 @@
 #!/bin/bash
 
-echo ">>> Testing $meta_functionality_name"
+echo ">>> Testing $meta_executable"
 
-tar -xavf $meta_resources_dir/rsem.tar.gz
+gunzip "${meta_resources_dir}/test_data/rsem.tar.gz"
+tar -xf "${meta_resources_dir}/test_data/rsem.tar"
 
 echo ">>> Calculating expression"
 "$meta_executable" \
   --id WT_REP1 \
   --strandedness reverse \
   --paired true \
-  --input "$meta_resources_dir/SRR6357070_1.fastq.gz,$meta_resources_dir/SRR6357070_2.fastq.gz" \
+  --input "${meta_resources_dir}/test_data/SRR6357070_1.fastq.gz;${meta_resources_dir}/test_data/SRR6357070_2.fastq.gz" \
   --index rsem \
   --extra_args "--star --star-output-genome-bam --star-gzipped-read-file --estimate-rspd --seed 1" \
   --counts_gene WT_REP1.genes.results \
-  --counts_transctips WT_REP1.isoforms.results \
+  --counts_transcripts WT_REP1.isoforms.results \
   --stat WT_REP1.stat \
   --logs WT_REP1.log \
   --bam_star WT_REP1.STAR.genome.bam \

src/rsem/rsem_calculate_expression/test_data/script.sh

@@ -3,3 +3,14 @@
 wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/testdata/GSE110004/SRR6357070_1.fastq.gz
 wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/testdata/GSE110004/SRR6357070_2.fastq.gz
 
+# decompress file without keeping the original
+gunzip SRR6357070_1.fastq.gz
+gunzip SRR6357070_2.fastq.gz
+
+# only keep 100 reads per file
+head -n 400 SRR6357070_1.fastq > SRR6357070_1.fastq.tmp
+head -n 400 SRR6357070_2.fastq > SRR6357070_2.fastq.tmp
+
+mv SRR6357070_1.fastq.tmp SRR6357070_1.fastq
+mv SRR6357070_2.fastq.tmp SRR6357070_2.fastq
+