src/nf_modules/porechop/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 version = "0.2.4"
 container_url = "lbmc/porechop:${version}"
 

src/nf_modules/rasusa/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 version = "0.6.0"
 container_url = "lbmc/rasusa:${version}"
 

src/nf_modules/rasusa/test.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 nextflow.enable.dsl=2
 
 /*

src/nf_modules/rasusa/test.sh

 #! /bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 ./nextflow src/nf_modules/rasusa/test.nf -c src/nextflow.config -profile docker --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" --fastq "data/tiny_dataset/fastq/tiny_R1.fastq"
 ./nextflow src/nf_modules/rasusa/test.nf -c src/nextflow.config -profile docker --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" --coverage 1.0
 ./nextflow src/nf_modules/rasusa/test.nf -c src/nextflow.config -profile docker --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" --fastq "data/tiny_dataset/fastq/tiny_R1.fastq" --size "1Mb"
\ No newline at end of file

src/nf_modules/salmon/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 version = "1.8.0"
 container_url = "lbmc/salmon:${version}"
 

src/nf_modules/sambamba/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 version = "0.6.7"
 container_url = "lbmc/sambamba:${version}"
 

src/nf_modules/samtools/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 version = "1.11"
 container_url = "lbmc/samtools:${version}"
 

src/nf_modules/sanity/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 container_url="mlepetit/sanity:latest"
 
 params.sanity_out=""

src/nf_modules/sratoolkit/list-srr.txt.license

+SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+
+SPDX-License-Identifier: CC-BY-SA-4.0

src/nf_modules/sratoolkit/main.nf

-version = "2.8.2"
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
+version = "3.0.0"
 container_url = "lbmc/sratoolkit:${version}"
 
 params.fastq_dump = ""

src/nf_modules/star/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 // STAR is an ultrafast universal RNA-seq aligner
 // 
 // EXAMPLE:

src/nf_modules/stringtie2/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 version = "2.1.1"
 container_url = "lbmc/stringtie2:${version}"
 

src/nf_modules/trinity/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
+version = "2.13.2"
+container_url = "lbmc/trinity:${version}"
+
+params.sample = 3
+params.min_glue = 1
+params.min_contig_length = 200
+params.assembly_out = ""
+
+
+workflow assembly {
+  take:
+    fastq
+  main:
+    complete_assembly(fastq)
+    super_transcript(complete_assembly.out.fasta)
+
+  emit:
+    fasta = complete_assembly.out.fasta
+    super_transcript = super_transcript.out.fasta
+}
+
+process complete_assembly {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$file_id"
+  if (params.assembly_out != "") {
+    publishDir "results/${params.assembly_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(file_id), path(fastq)
+
+  output:
+    tuple val(file_id), path("trinity_output_${file_prefix}/"), emit: folder
+    tuple val(file_id), path("trinity_output_${file_prefix}.Trinity.fasta"), emit: fasta
+    tuple val(file_id), path("trinity_output_${file_prefix}.Trinity.fasta.gene_trans_map"), emit: gene_map 
+    tuple val(file_id), path("trinity_output_${file_prefix}/salmon_outdir/quant.sf"), emit: quant
+
+  script:
+
+  switch(file_id) {
+    case {it instanceof List}:
+      file_prefix = file_id[0]
+    break;
+    case {it instanceof Map}:
+      file_prefix = file_id.values()[0]
+    break;
+    default:
+      file_prefix = file_id
+    break;
+  };
+  def memory = "${task.memory}" - ~/\s*GB/
+
+  if (fastq.size() == 2)
+"""
+  mkdir trinity_output_${file_prefix}
+  Trinity \
+    --seqType fq \
+    --max_memory ${memory}G \
+    --left ${fastq[0]} \
+    --right ${fastq[1]} \
+    --CPU ${task.cpus} \
+    --min_glue ${params.min_glue} \
+    --min_contig_length ${params.min_contig_length} \
+    --output trinity_output_${file_prefix}
+"""
+  else
+"""
+  mkdir trinity_output_${file_prefix}
+  Trinity \
+    --seqType fq \
+    --max_memory ${memory}G \
+    --single ${fastq} \
+    --CPU ${task.cpus} \
+    --min_glue ${params.min_glue} \
+    --min_contig_length ${params.min_contig_length} \
+    --output trinity_output_${file_prefix}
+"""
+}
+
+
+process super_transcript {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "$file_id"
+  if (params.assembly_out != "") {
+    publishDir "results/${params.assembly_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(file_id), path(fasta)
+
+  output:
+    tuple val(file_id), path("trinity_genes.fasta"), path("trinity_genes.gtf"), emit: fasta
+
+  script:
+
+  switch(file_id) {
+    case {it instanceof List}:
+      file_prefix = file_id[0]
+    break;
+    case {it instanceof Map}:
+      file_prefix = file_id.values()[0]
+    break;
+    default:
+      file_prefix = file_id
+    break;
+  };
+  def memory = "${task.memory}" - ~/\s*GB/
+
+"""
+Trinity_gene_splice_modeler.py \
+  --trinity_fasta ${fasta}
+"""
+}

src/nf_modules/ucsc/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 version = "407"
 container_url = "lbmc/ucsc:${version}"
 

src/nf_modules/urqt/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 version = "d62c1f8"
 container_url = "lbmc/urqt:${version}"
 

src/solution_RNASeq.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 nextflow.enable.dsl=2
 
 include { fastp } from "./nf_modules/fastp/main.nf"

src/training_dataset.config

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 profiles {
   docker {
     docker.temp = "auto"

src/training_dataset.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 /*
 small pipeline to build a training dataset from whole genome data