From 82b23bb29833cd29897c2377d7f4944800c0a34e Mon Sep 17 00:00:00 2001
From: christopher-hakkaart <chris.hakkaart@seqera.io>
Date: Mon, 9 Sep 2024 13:43:53 +0200
Subject: [PATCH] Create example branch

Signed-off-by: christopher-hakkaart <chris.hakkaart@seqera.io>
---
 bin/fastqc.sh               |   6 --
 conda.yml                   |  10 ---
 docker/Docker.s3            |   3 -
 docker/Dockerfile           |  16 -----
 docker/Makefile             |  10 ---
 main.nf                     | 133 +++++++++++++++++++++++++++-------
 modules/fastqc/main.nf      |  18 -----
 modules/index/main.nf       |  16 -----
 modules/multiqc/main.nf     |  20 ------
 modules/quant/main.nf       |  17 -----
 modules/rnaseq.nf           |  19 -----
 multiqc/logo.png            | Bin 22121 -> 0 bytes
 multiqc/multiqc_config.yaml |  11 ---
 nextflow.config             | 137 +-----------------------------------
 nextflow_schema.json        |  14 +---
 15 files changed, 110 insertions(+), 320 deletions(-)
 delete mode 100755 bin/fastqc.sh
 delete mode 100644 conda.yml
 delete mode 100644 docker/Docker.s3
 delete mode 100644 docker/Dockerfile
 delete mode 100644 docker/Makefile
 delete mode 100644 modules/fastqc/main.nf
 delete mode 100644 modules/index/main.nf
 delete mode 100644 modules/multiqc/main.nf
 delete mode 100644 modules/quant/main.nf
 delete mode 100644 modules/rnaseq.nf
 delete mode 100755 multiqc/logo.png
 delete mode 100755 multiqc/multiqc_config.yaml

diff --git a/bin/fastqc.sh b/bin/fastqc.sh
deleted file mode 100755
index 93f38b6..0000000
--- a/bin/fastqc.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env bash
-sample_id="$1"
-reads="$2"
-
-mkdir fastqc_${sample_id}_logs
-fastqc -o fastqc_${sample_id}_logs -f fastq -q ${reads}
diff --git a/conda.yml b/conda.yml
deleted file mode 100644
index 8ed4151..0000000
--- a/conda.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-name: rnaseq-nf
-channels:
-  - seqera
-  - bioconda
-  - conda-forge
-  - defaults
-dependencies:
-  - salmon=1.10.2
-  - fastqc=0.12.1
-  - multiqc=1.15
diff --git a/docker/Docker.s3 b/docker/Docker.s3
deleted file mode 100644
index 910ad17..0000000
--- a/docker/Docker.s3
+++ /dev/null
@@ -1,3 +0,0 @@
-FROM nextflow/rnaseq-nf:latest 
-
-RUN conda install -y awscli
\ No newline at end of file
diff --git a/docker/Dockerfile b/docker/Dockerfile
deleted file mode 100644
index f6147f8..0000000
--- a/docker/Dockerfile
+++ /dev/null
@@ -1,16 +0,0 @@
-FROM mambaorg/micromamba
-MAINTAINER Paolo Di Tommaso <paolo.ditommaso@gmail.com>
-
-RUN \
-   micromamba install -y -n base -c defaults -c bioconda -c conda-forge \
-      salmon=1.10.2 \
-      fastqc=0.12.1 \
-      multiqc=1.17 \
-      python=3.11 \
-      typing_extensions \
-      importlib_metadata \
-      procps-ng \
-   && micromamba clean -a -y
-
-ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
-USER root
diff --git a/docker/Makefile b/docker/Makefile
deleted file mode 100644
index 8cc51da..0000000
--- a/docker/Makefile
+++ /dev/null
@@ -1,10 +0,0 @@
-version ?= v1.2.1
-
-all: build push
-
-build:
-	cp ../conda.yml .
-	docker build --output=type=docker --progress=plain --tag quay.io/nextflow/rnaseq-nf:${version} .
-	
-push:
-	docker push quay.io/nextflow/rnaseq-nf:${version}
diff --git a/main.nf b/main.nf
index 5cc1280..3a4af3f 100755
--- a/main.nf
+++ b/main.nf
@@ -1,37 +1,116 @@
-#!/usr/bin/env nextflow 
+#!/usr/bin/env nextflow
 
 /*
- * Proof of concept of a RNAseq pipeline implemented with Nextflow
+ * Pipeline parameters
  */
 
+// Input data
+params.reads = "${workflow.projectDir}/data/ggal/ggal_gut_{1,2}.fq"
+
+// Reference file
+params.transcriptome = "${workflow.projectDir}/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
+
+// Output directory
+params.outdir = "results"
 
 /*
- * Default pipeline parameters. They can be overriden on the command line eg.
- * given `params.foo` specify on the run command line `--foo some_value`.
+ * Index reference transcriptome file
  */
+process INDEX {
+    tag "$transcriptome.simpleName"
+    container "community.wave.seqera.io/library/salmon:1.10.3--482593b6cd04c9b7"
+    conda "bioconda::salmon=1.10.3"
 
-params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
-params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
-params.outdir = "results"
-params.multiqc = "$baseDir/multiqc"
-
-log.info """\
- R N A S E Q - N F   P I P E L I N E
- ===================================
- transcriptome: ${params.transcriptome}
- reads        : ${params.reads}
- outdir       : ${params.outdir}
- """
-
-// import modules
-include { RNASEQ } from './modules/rnaseq'
-include { MULTIQC } from './modules/multiqc'
-
-/* 
- * main script flow
+    input:
+    path transcriptome
+
+    output:
+    path 'index'
+
+    script:
+    """
+    salmon index --threads $task.cpus -t $transcriptome -i index
+    """
+}
+
+/*
+ * Generate FastQC reports
  */
-workflow {
-  read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true ) 
-  RNASEQ( params.transcriptome, read_pairs_ch )
-  MULTIQC( RNASEQ.out, params.multiqc )
+process FASTQC {
+    tag "FASTQC on $sample_id"
+    publishDir params.outdir, mode:'copy'
+    container "community.wave.seqera.io/library/fastqc:0.12.1--5cfd0f3cb6760c42"
+    conda "bioconda::fastqc:0.12.1"
+
+    input:
+    tuple val(sample_id), path(reads)
+
+    output:
+    path "fastqc_${sample_id}_logs"
+
+    script:
+    """
+    mkdir fastqc_${sample_id}_logs
+    fastqc -o fastqc_${sample_id}_logs -f fastq -q ${reads}
+    """
+}
+
+/*
+ * Quantify reads
+ */
+process QUANT {
+    tag "$pair_id"
+    publishDir params.outdir, mode:'copy'
+    container "community.wave.seqera.io/library/salmon:1.10.3--482593b6cd04c9b7"
+    conda "bioconda::salmon=1.10.3"
+
+    input:
+    path index
+    tuple val(pair_id), path(reads)
+
+    output:
+    path pair_id
+
+    script:
+    """
+    salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
+    """
 }
+
+/*
+ * Generate MultiQC report
+ */
+process MULTIQC {
+  publishDir params.outdir, mode:'copy'
+    container "community.wave.seqera.io/library/multiqc:1.24.1--789bc3917c8666da"
+    conda "bioconda::multiqc:1.24.1"
+
+    input:
+    path '*'
+
+    output:
+    path 'multiqc_report.html'
+
+    script:
+    """
+    multiqc .
+    """
+}
+
+workflow {
+
+    // Paired reference data
+    read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
+
+    // Index reference transcriptome file
+    INDEX(params.transcriptome)
+
+    // Generate FastQC reports
+    FASTQC(read_pairs_ch)
+
+    // Quantify reads
+    QUANT(INDEX.out, read_pairs_ch)
+
+    // Generate MultiQC report
+    MULTIQC(QUANT.out.mix(FASTQC.out).collect())
+}
\ No newline at end of file
diff --git a/modules/fastqc/main.nf b/modules/fastqc/main.nf
deleted file mode 100644
index 57c0477..0000000
--- a/modules/fastqc/main.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-params.outdir = 'results'
-
-process FASTQC {
-    tag "FASTQC on $sample_id"
-    conda 'bioconda::fastqc=0.12.1'
-    publishDir params.outdir, mode:'copy'
-
-    input:
-    tuple val(sample_id), path(reads)
-
-    output:
-    path "fastqc_${sample_id}_logs", emit: logs
-
-    script:
-    """
-    fastqc.sh "$sample_id" "$reads"
-    """
-}
diff --git a/modules/index/main.nf b/modules/index/main.nf
deleted file mode 100644
index 72187c8..0000000
--- a/modules/index/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-
-process INDEX {
-    tag "$transcriptome.simpleName"
-    conda 'bioconda::salmon=1.10.2'
-    
-    input:
-    path transcriptome 
-
-    output:
-    path 'index' 
-
-    script:
-    """
-    salmon index --threads $task.cpus -t $transcriptome -i index
-    """
-}
diff --git a/modules/multiqc/main.nf b/modules/multiqc/main.nf
deleted file mode 100644
index 408d53b..0000000
--- a/modules/multiqc/main.nf
+++ /dev/null
@@ -1,20 +0,0 @@
-params.outdir = 'results'
-
-process MULTIQC {
-    conda 'bioconda::multiqc=1.17'
-    publishDir params.outdir, mode:'copy'
-
-    input:
-    path '*'
-    path 'config'
-
-    output:
-    path 'multiqc_report.html', emit: report
-
-    script:
-    """
-    cp $config/* .
-    echo "custom_logo: \$PWD/logo.png" >> multiqc_config.yaml
-    multiqc -o multiqc_report.html .
-    """
-}
diff --git a/modules/quant/main.nf b/modules/quant/main.nf
deleted file mode 100644
index a873ddb..0000000
--- a/modules/quant/main.nf
+++ /dev/null
@@ -1,17 +0,0 @@
-
-process QUANT {
-    tag "$pair_id"
-    conda 'bioconda::salmon=1.10.2'
-
-    input:
-    path index 
-    tuple val(pair_id), path(reads) 
-
-    output:
-    path pair_id 
-
-    script:
-    """
-    salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
-    """
-}
diff --git a/modules/rnaseq.nf b/modules/rnaseq.nf
deleted file mode 100644
index 2f607c1..0000000
--- a/modules/rnaseq.nf
+++ /dev/null
@@ -1,19 +0,0 @@
-params.outdir = 'results'
-
-include { INDEX } from './index'
-include { QUANT } from './quant'
-include { FASTQC } from './fastqc'
-
-workflow RNASEQ {
-  take:
-    transcriptome
-    read_pairs_ch
- 
-  main: 
-    INDEX(transcriptome)
-    FASTQC(read_pairs_ch)
-    QUANT(INDEX.out, read_pairs_ch)
-
-  emit: 
-     QUANT.out | concat(FASTQC.out) | collect
-}
\ No newline at end of file
diff --git a/multiqc/logo.png b/multiqc/logo.png
deleted file mode 100755
index 08a19e4d8cbd61ac6555c12cc2c7139da4bf6151..0000000000000000000000000000000000000000
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diff --git a/multiqc/multiqc_config.yaml b/multiqc/multiqc_config.yaml
deleted file mode 100755
index 041fb0b..0000000
--- a/multiqc/multiqc_config.yaml
+++ /dev/null
@@ -1,11 +0,0 @@
-title: "Nextflow RNA-seq demo"
-subtitle: "A pipeline for quantification of genomic features from short read data"
-
-report_header_info:
-    - Contact E-mail: 'paolo.ditommaso@gmail.com'
-    - Application Type: 'RNA-seq'
-    - Project Type: 'Nextflow demo'
-
-custom_logo_url: 'https://www.nextflow.io'
-custom_logo_title: 'Center for Genomic Regulation'
-
diff --git a/nextflow.config b/nextflow.config
index e1297da..d3af3ea 100755
--- a/nextflow.config
+++ b/nextflow.config
@@ -1,136 +1 @@
-/*
- * Copyright (c) 2013-2023, Seqera Labs.
- *
- * This Source Code Form is subject to the terms of the Mozilla Public
- * License, v. 2.0. If a copy of the MPL was not distributed with this
- * file, You can obtain one at http://mozilla.org/MPL/2.0/.
- *
- * This Source Code Form is "Incompatible With Secondary Licenses", as
- * defined by the Mozilla Public License, v. 2.0.
- *
- */
- 
-manifest {
-  description = 'Proof of concept of a RNA-seq pipeline implemented with Nextflow' 
-  author = 'Paolo Di Tommaso'
-  nextflowVersion = '>=23.10.0'
-}
-
-/* 
- * default params 
- */
- 
-params.outdir = "results"
-params.reads = "${projectDir}/data/ggal/ggal_gut_{1,2}.fq"
-params.transcriptome = "${projectDir}/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
-params.multiqc = "${projectDir}/multiqc"
-
-/* 
- * defines execution profiles for different environments  
- */ 
-
-profiles {
-  standard {
-    process.container = 'quay.io/nextflow/rnaseq-nf:v1.2.1'
-  }
-
-  'all-reads' {
-    params.reads = "${projectDir}/data/ggal/ggal_*_{1,2}.fq"
-  }
-
-  /*
-   * NOTE: requires nextflow 24.03.0-edge or later
-   */
-  wave {
-    wave.enabled = true
-    wave.strategy = 'conda'
-    wave.freeze = true
-  }
-
-  docker {
-    process.container = 'quay.io/nextflow/rnaseq-nf:v1.2.1'
-    docker.enabled = true
-  }
-
-  singularity {
-    process.container = 'quay.io/nextflow/rnaseq-nf:v1.2.1'
-    singularity.enabled = true
-    singularity.autoMounts = true
-  }
-
-  conda {
-    conda.enabled = true
-    conda.channels = 'seqera,conda-forge,bioconda,defaults'
-  }
-  
-  slurm {
-    process.container = 'quay.io/nextflow/rnaseq-nf:v1.2.1'
-    process.executor = 'slurm'
-    singularity.enabled = true
-  }
-  
-  batch {
-    params.reads = 's3://rnaseq-nf/data/ggal/lung_{1,2}.fq'
-    params.transcriptome = 's3://rnaseq-nf/data/ggal/transcript.fa'
-    process.container = 'quay.io/nextflow/rnaseq-nf:v1.2.1'
-    process.executor = 'awsbatch'
-    process.queue = 'nextflow-ci'
-    workDir = 's3://nextflow-ci/work'
-    aws.region = 'eu-west-1'
-    aws.batch.cliPath = '/home/ec2-user/miniconda/bin/aws'
-  }
-
-  's3-data' {
-    process.container = 'quay.io/nextflow/rnaseq-nf:v1.2.1'
-    params.reads = 's3://rnaseq-nf/data/ggal/lung_{1,2}.fq'
-    params.transcriptome = 's3://rnaseq-nf/data/ggal/transcript.fa'
-  } 
-
-  gls {
-      params.transcriptome = 'gs://rnaseq-nf/data/ggal/transcript.fa'
-      params.reads = 'gs://rnaseq-nf/data/ggal/gut_{1,2}.fq'
-      params.multiqc = 'gs://rnaseq-nf/multiqc'
-      process.executor = 'google-lifesciences'
-      process.container = 'quay.io/nextflow/rnaseq-nf:v1.2.1'
-      workDir = 'gs://rnaseq-nf/scratch' // <- replace with your own bucket!
-      google.region  = 'europe-west2'
-  } 
-  
-  gcb {
-      params.transcriptome = 'gs://rnaseq-nf/data/ggal/transcript.fa'
-      params.reads = 'gs://rnaseq-nf/data/ggal/gut_{1,2}.fq'
-      params.multiqc = 'gs://rnaseq-nf/multiqc'
-      process.executor = 'google-batch'
-      process.container = 'quay.io/nextflow/rnaseq-nf:v1.2.1'
-      workDir = 'gs://rnaseq-nf/scratch' // <- replace with your own bucket!
-      google.region  = 'europe-west2'
-  }
-
-  'gs-data' {
-      process.container = 'quay.io/nextflow/rnaseq-nf:v1.2.1'
-      params.transcriptome = 'gs://rnaseq-nf/data/ggal/transcript.fa'
-      params.reads = 'gs://rnaseq-nf/data/ggal/gut_{1,2}.fq'
-  }
-
-  azb {
-    process.container = 'quay.io/nextflow/rnaseq-nf:v1.2.1'
-    workDir = 'az://nf-scratch/work'
-    process.executor = 'azurebatch'
-    process.queue = 'nextflow-ci' // replace with your own Azure pool name
-
-    azure {
-      batch {
-        location = 'westeurope'
-        accountName = "$AZURE_BATCH_ACCOUNT_NAME" 
-        accountKey = "$AZURE_BATCH_ACCOUNT_KEY"
-        autoPoolMode = true
-        deletePoolsOnCompletion = true
-      }
-
-      storage {
-        accountName = "$AZURE_STORAGE_ACCOUNT_NAME"
-        accountKey = "$AZURE_STORAGE_ACCOUNT_KEY"
-      }
-    }
-  }
-}
+docker.enabled = true
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 823417a..7ca8950 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -15,25 +15,17 @@
           "type": "string",
           "format": "directory-path",
           "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
-          "fa_icon": "fas fa-folder-open",
-          "default": "results"
+          "fa_icon": "fas fa-folder-open"
         },
         "reads": {
           "type": "string",
           "description": "The input read-pair files",
-          "fa_icon": "fas fa-folder-open",
-          "default": "${projectDir}/data/ggal/ggal_gut_{1,2}.fq"
+          "fa_icon": "fas fa-folder-open"
         },
         "transcriptome": {
           "type": "string",
           "description": "The input transcriptome file",
-          "fa_icon": "fas fa-folder-open",
-          "default": "${projectDir}/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
-        },
-        "multiqc": {
-          "type": "string",
-          "fa_icon": "fas fa-folder-open",
-          "default": "${projectDir}/multiqc"
+          "fa_icon": "fas fa-folder-open"
         }
       }
     }