Re-add trimgalore into monorepo

Merge remote-tracking branch 'trimgalore-origin/master'

src/trimgalore/.gitattributes

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+notebooks/* linguist-vendored

src/trimgalore/.gitignore

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+*checkpoint.ipynb
+*checkpoint*
+*checkpoint.py
+*.test.ipynb
+*.csv
+*.loom
+*.pickle
+*.pyc
+*.html
+*egg*
+.vscode
+.nextflow
+.nextflow*
+data
+refdata
+work
+out/notebooks
+src/scenic/out
+src/scenic/notebooks
+src/scenic/data
+refdata
+data/10x/tiny
+work/
+out/
+tests/
+debug/
+*.swp
+*.swo

src/trimgalore/Dockerfile

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+FROM python:3.7-slim
+
+ENV DEBIAN_FRONTEND=noninteractive
+RUN BUILDPKGS="build-essential zlib1g-dev git curl" && \
+    apt-get update && \
+    apt-get install -y --no-install-recommends apt-utils debconf locales && dpkg-reconfigure locales && \
+    apt-get install -y --no-install-recommends $BUILDPKGS
+
+RUN pip install -U pip
+
+##################################################
+# cutadapt
+RUN pip install cutadapt
+
+##################################################
+# fastQC
+# RUN wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.9.zip
+
+##################################################
+# trim galore
+RUN curl -fsSL https://github.com/FelixKrueger/TrimGalore/archive/0.6.6.tar.gz -o trim_galore.tar.gz && \
+    tar xvzf trim_galore.tar.gz && \
+    mv TrimGalore-0.6.6/trim_galore /usr/bin/ && \
+    rm -r TrimGalore-0.6.6
+
+
+RUN apt-get -y update && \
+    apt-get -y --no-install-recommends install \
+        # Need to run ps
+        procps \
+        pigz \
+        less && \
+    rm -rf /var/cache/apt/* && \
+    rm -rf /var/lib/apt/lists/*
+

src/trimgalore/README.rst

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+
+Trim Galore module
+==================
+
+This repository contains an implementation of Trim Galore for VIB-SingleCell-NF (VSN) pipelines.
+See `here <https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/>`_ for the original source.
+

src/trimgalore/main.nf

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+nextflow.preview.dsl=2
+
+//////////////////////////////////////////////////////
+//  Import sub-workflows from the modules:
+
+include SC__FILE_CONVERTER from '../utils/processes/utils.nf' params(params)
+
+include SC__TEMPLATE__PROCESS1 from './processes/process1.nf' params(params)
+
+
+//////////////////////////////////////////////////////
+// Define the workflow
+
+workflow template {
+
+    take:
+        data
+
+    main:
+        data = SC__FILE_CONVERTER(data)
+        data.view()
+
+        SC__TEMPLATE__PROCESS1(data)
+
+}
+

src/trimgalore/processes/trim.nf

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+nextflow.preview.dsl=2
+
+// binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/template/bin/" : ""
+
+toolParams = params.tools.trimgalore
+
+process SC__TRIMGALORE__TRIM {
+
+    container toolParams.container
+    label 'compute_resources__cpu','compute_resources__24hqueue'
+
+    input:
+        tuple val(sampleId),
+              path(fastq_PE1),
+              path(fastq_PE2)
+
+    output:
+        tuple val(sampleId),
+              path("${sampleId}_dex_R1_val_1.fq.gz"),
+              path("${sampleId}_dex_R2_val_2.fq.gz"),
+              path("${sampleId}_dex_R1.fastq.gz_trimming_report.txt"),
+              path("${sampleId}_dex_R2.fastq.gz_trimming_report.txt")
+
+    script:
+        def sampleParams = params.parseConfig(sampleId, params.global, toolParams.trim)
+        processParams = sampleParams.local
+        """
+        trim_galore \
+            -j ${task.cpus} \
+            -o . \
+            ${fastq_PE1} \
+            ${fastq_PE2} \
+            --paired \
+            --gzip
+        """
+}
+

src/trimgalore/trimgalore.config

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+params {
+    tools {
+        trimgalore {
+            container = 'vibsinglecellnf/trimgalore:0.6.6'
+            trim {
+                paired = 'true'
+            }
+        }
+    }
+}
+