three rsem components initial commit

src/rsem/rsem_calculate_expression/config.vsh.yaml

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+name: "rsem_calculate_expression"
+namespace: "rsem"
+description: | 
+  Calculate expression with RSEM.
+keywords: ["Transcriptome", "Index"]
+links:
+  homepage: https://deweylab.github.io/RSEM/
+  documentation: https://deweylab.github.io/RSEM/rsem-calculate-expression.html
+  repository: https://github.com/deweylab/RSEM
+references: 
+  doi: https://doi.org/10.1186/1471-2105-12-323
+license: GPL-3.0
+
+
+argument_groups:
+- name: "Input"
+  arguments:
+  - name: "--id"
+    type: string
+    description: Sample ID.
+  - name: "--strandedness"
+    type: string
+    description: Sample strand-specificity. Must be one of unstranded, forward, reverse
+    choices: [forward, reverse, unstranded]
+  - name: "--paired"
+    type: boolean
+    description: Paired-end reads or not?
+  - name: "--input"
+    type: file
+    description: Input reads for quantification.
+    multiple: true
+  - name: "--index"
+    type: file
+    description: RSEM index.  
+  - name: "--extra_args"
+    type: string
+    description: Extra rsem-calculate-expression arguments in addition to the examples.
+
+- name: "Output"
+  arguments:
+  - name: "--counts_gene"
+    type: file
+    description: Expression counts on gene level
+    example: $id.genes.results
+    direction: output
+  - name: "--counts_transcripts"
+    type: file
+    description: Expression counts on transcript level
+    example: $id.isoforms.results
+    direction: output
+  - name: "--stat"
+    type: file
+    description: RSEM statistics
+    example: $id.stat
+    direction: output
+  - name: "--logs"
+    type: file
+    description: RSEM logs
+    example: $id.log
+    direction: output
+  - name: "--bam_star"
+    type: file
+    description: BAM file generated by STAR (optional)
+    example: $id.STAR.genome.bam
+    direction: output
+  - name: "--bam_genome"
+    type: file
+    description: Genome BAM file (optional)
+    example: $id.genome.bam
+    direction: output
+  - name: "--bam_transcript"
+    type: file
+    description: Transcript BAM file (optional)
+    example: $id.transcript.bam
+    direction: output
+
+resources:
+  - type: bash_script
+    path: script.sh
+
+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 
+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
+runners:
+  - type: executable
+  - type: nextflow

src/rsem/rsem_calculate_expression/script.sh

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+#!/bin/bash
+
+set -eo pipefail
+
+function clean_up {
+    rm -rf "$tmpdir"
+}
+trap clean_up EXIT
+
+tmpdir=$(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'
+else
+    strandedness=''
+fi
+
+IFS="," read -ra input <<< $par_input
+
+INDEX=$(find -L $meta_resources_dir/ -name "*.grp" | sed 's/\.grp$//')
+
+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

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+#!/bin/bash
+
+echo ">>> Testing $meta_functionality_name"
+
+tar -xavf $meta_resources_dir/rsem.tar.gz
+
+echo ">>> Calculating expression"
+"$meta_executable" \
+  --id WT_REP1 \
+  --strandedness reverse \
+  --paired true \
+  --input "$meta_resources_dir/SRR6357070_1.fastq.gz,$meta_resources_dir/SRR6357070_2.fastq.gz" \
+  --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 \
+  --stat WT_REP1.stat \
+  --logs WT_REP1.log \
+  --bam_star WT_REP1.STAR.genome.bam \
+  --bam_genome WT_REP1.genome.bam \
+  --bam_transcript WT_REP1.transcript.bam 
+
+echo ">>> Checking whether output exists"
+[ ! -f "WT_REP1.genes.results" ] && echo "Gene level expression counts file does not exist!" && exit 1
+[ ! -s "WT_REP1.genes.results" ] && echo "Gene level expression counts file is empty!" && exit 1
+[ ! -f "WT_REP1.isoforms.results" ] && echo "Transcript level expression counts file does not exist!" && exit 1
+[ ! -s "WT_REP1.isoforms.results" ] && echo "Transcript level expression counts file is empty!" && exit 1
+[ ! -f "WT_REP1.stat" ] && echo "Stats file does not exist!" && exit 1
+[ ! -s "WT_REP1.stat" ] && echo "Stats file is empty!" && exit 1
+[ ! -f "WT_REP1.log" ] && echo "Log file does not exist!" && exit 1
+[ ! -s "WT_REP1.log" ] && echo "Log file is empty!" && exit 1
+
+echo "All tests succeeded!"
+exit 0

src/rsem/rsem_calculate_expression/test_data/script.sh

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+#!/bin/bash
+
+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
+

src/rsem/rsem_merge_counts/config.vsh.yaml

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+name: "rsem_merge_counts"
+namespace: "rsem"
+info:
+  migration_info:
+    git_repo: https://github.com/nf-core/rnaseq.git
+    paths: [modules/local/rsem_merge_counts/main.nf]
+    last_sha: 311279532694ce7520164ce4d65a388c0cd11f60
+
+description: | 
+  Merge the transcript quantification results obtained from rsem calculate-expression across all samples.
+
+argument_groups:
+- name: "Input"
+  arguments:
+  - name: "--counts_gene"
+    type: file
+    description: Expression counts on gene level (genes)
+  - name: "--counts_transcripts"
+    type: file
+    description: Expression counts on transcript level (isoforms)
+  - name: "--versions"
+    type: file
+    must_exist: false
+
+- name: "Output"
+  arguments: 
+  - name: "--merged_gene_counts"
+    type: file
+    description: File containing gene counts across all samples.
+    default: rsem.merged.gene_counts.tsv
+    direction: output
+  - name: "--merged_gene_tpm"
+    type: file
+    description: File containing gene TPM across all samples.
+    default: rsem.merged.gene_tpm.tsv
+    direction: output
+  - name: "--merged_transcript_counts"
+    type: file
+    description: File containing transcript counts across all samples.
+    default: rsem.merged.transcript_counts.tsv
+    direction: output
+  - name: "--merged_transcript_tpm"
+    type: file
+    description: File containing transcript TPM across all samples.
+    default: rsem.merged.transcript_tpm.tsv
+    direction: output
+  - name: "--updated_versions"
+    type: file
+    default: versions.yml
+    direction: output
+
+resources:
+  - type: bash_script
+    path: script.sh
+
+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
+
+engines:
+  - type: docker
+    image: ubuntu:22.04
+
+runners:
+  - type: executable
+  - type: nextflow

src/rsem/rsem_merge_counts/help.txt

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+```bash
+rsem-merge-counts --help
+```

src/rsem/rsem_merge_counts/script.sh

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+#!/bin/bash
+
+set -ep pipefail
+
+mkdir -p tmp/genes
+# cut -f 1,2 `ls $par_count_genes/*` | head -n 1` > gene_ids.txt
+for file_id in ${par_count_genes[*]}; do
+    samplename=$(basename $file_id | sed s/\\.genes.results\$//g)
+    echo $samplename > tmp/genes/${samplename}.counts.txt
+    cut -f 5 ${file_id} | tail -n+2 >> tmp/genes/${samplename}.counts.txt
+    echo $samplename > tmp/genes/${samplename}.tpm.txt
+    cut -f 6 ${file_id} | tail -n+2 >> tmp/genes/${samplename}.tpm.txt
+done
+
+mkdir -p tmp/isoforms
+# cut -f 1,2 `ls $par_counts_transcripts/*` | head -n 1` > transcript_ids.txt
+for file_id in ${par_counts_transcripts[*]}; do
+    samplename=$(basename $file_id | sed s/\\.isoforms.results\$//g)
+    echo $samplename > tmp/isoforms/${samplename}.counts.txt
+    cut -f 5 ${file_id} | tail -n+2 >> tmp/isoforms/${samplename}.counts.txt
+    echo $samplename > tmp/isoforms/${samplename}.tpm.txt
+    cut -f 6 ${file_id} | tail -n+2 >> tmp/isoforms/${samplename}.tpm.txt
+done
+
+paste gene_ids.txt tmp/genes/*.counts.txt > $par_merged_gene_counts
+paste gene_ids.txt tmp/genes/*.tpm.txt > $par_merged_gene_tpm
+paste transcript_ids.txt tmp/isoforms/*.counts.txt > $par_merged_transcript_counts
+paste transcript_ids.txt tmp/isoforms/*.tpm.txt > $par_merged_transcript_tpm
+
+# Version
+text="${meta_functionality_name}:
+    sed: $(echo $(sed --version 2>&1) | grep -oP 'sed \(GNU sed\) \K\d+\.\d+')"
+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_merge_counts/test_data/script.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+
+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
+wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/rsem.tar.gz
+

src/rsem/rsem_prepare_reference/config.vsh.yaml

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+name: "rsem_prepare_reference"
+namespace: "rsem"
+info:
+  migration_info:
+    git_repo: https://github.com/nf-core/rnaseq.git
+    paths: [modules/nf-core/rsem/preparereference/main.nf, modules/nf-core/rsem/preparereference/meta.yml]
+    last_sha: 92b2a7857de1dda9d1c19a088941fc81e2976ff7
+
+description: | 
+  Prepare a reference genome for RSEM.
+
+argument_groups:
+- name: "Input"
+  arguments: 
+  - name: "--fasta"
+    type: file
+    description: Genome fasta file
+  - name: "--gtf"
+    type: file
+    description: GTF file
+  - name: "--star"
+    type: boolean
+  - name: "--versions"
+    type: file
+    must_exist: false
+
+- name: "Output"
+  arguments: 
+  - name: "--rsem"
+    type: file
+    direction: output
+    description: RSEM index directory.
+  - name: "--transcript_fasta"
+    type: file
+    direction: output
+    description: Fasta file of transcripts
+  - name: "--updated_versions"
+    type: file
+    default: versions.yml
+    direction: output
+
+resources:
+  - type: bash_script
+    path: script.sh
+
+test_resources:
+  - type: bash_script
+    path: test.sh
+  - path: /testData/minimal_test/reference/genome.fasta
+  - path: /testData/minimal_test/reference/genes.gtf.gz
+
+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
+runners: 
+- type: executable
+- type: nextflow