src/nf_modules/fastq_screen/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
+version = "0.11.3--pl5.22.0_0"
+container_url = "quay.io/biocontainers/fastq-screen:${version}"
+
+params.fastq_screen = ""
+params.fastq_screen_out = ""
+process fastq_screen {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$file_id"
+  if (params.index_fasta_out != "") {
+    publishDir "results/${params.fastq_screen_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(file_id), path(fastq)
+
+  output:
+    tuple val(file_id), path("*"), emit: output
+
+  script:
+"""
+fastq_screen --get_genomes
+fastq_screen --threads ${task.cpus} sample1.fastq sample2.fastq
+"""
+}

src/nf_modules/fastqc/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 version = "0.11.5"
 container_url = "lbmc/fastqc:${version}"
 

src/nf_modules/flexi_splitter/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 version = "1.0.2"
 container_url = "lbmc/flexi_splitter:${version}"
 

src/nf_modules/flexi_splitter/marseq_flexi_splitter.yaml

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 PLATE:
   coords:
     reads: 0

src/nf_modules/flexi_splitter/toy_file_paired.yaml

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 PCR:
   coords:
     reads: 3

src/nf_modules/g2gtools/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 version = "0.2.8"
 container_url = "lbmc/g2gtools:${version}"
 

src/nf_modules/gatk3/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 version = "3.8.0"
 container_url = "lbmc/gatk:${version}"
 

src/nf_modules/gatk4/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 version = "4.2.0.0"
 container_url = "broadinstitute/gatk:${version}"
 

src/nf_modules/gffread/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 version = "0.12.2"
 container_url = "lbmc/gffread:${version}"
 

src/nf_modules/guppy-cpu/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 version = "5.0.11"
 container_url = "lbmc/guppy-cpu:${version}"
 

src/nf_modules/guppy-gpu/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 version = "5.0.11"
 container_url = "lbmc/guppy-gpu:${version}"
 

src/nf_modules/hisat2/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 version = "2.2.1"
 container_url = "lbmc/hisat2:${version}"
 

src/nf_modules/htseq/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
 
 version = "1.99.2"
 container_url = "lbmc/htseq:${version}"
@@ -23,7 +26,7 @@ gffread ${gff3_file} -T -o ${genome_id}.gtf
 
 process htseq_count {
     container = "${container_url}"
-    label "big_mem_multi_cpus"
+    label "big_mem_mono_cpus"
     tag "file_id: $file_id"
     if (params.htseq_out != "") {
         publishDir "results/${params.htseq_out}", mode: 'copy'

src/nf_modules/kallisto/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 version = "0.44.0"
 container_url = "lbmc/kallisto:${version}"
 

src/nf_modules/kb/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 version = "0.26.0"
 container_url = "lbmc/kb:${version}"
 

src/nf_modules/macs2/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 version = "2.1.2"
 container_url = "lbmc/macs2:${version}"
 

src/nf_modules/macs3/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 version = "3.0.0a6"
 container_url = "lbmc/macs3:${version}"
 

src/nf_modules/minimap2/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 version = "2.17"
 container_url = "lbmc/minimap2:${version}"
 

src/nf_modules/multiqc/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 // multiqc generate nice html report combining lots of differents bioinformatics
 // tools report.
 // 

src/nf_modules/picard/main.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 version = "2.18.11"
 container_url = "lbmc/picard:${version}"