src/docker_modules/SRAtoolkit/2.8.2/docker_init.sh

-#!/bin/sh
-docker build src/docker_modules/SRAtoolkit/2.8.2 -t 'sratoolkit:2.8.2'

src/docker_modules/Salmon/0.8.2/docker_init.sh

-#!/bin/sh
-docker build src/docker_modules/Salmon/0.8.2 -t 'salmon:0.8.2'

src/docker_modules/TopHat/2.1.1/Dockerfile

-FROM ubuntu:18.04
-MAINTAINER Laurent Modolo
-
-ENV TOPHAT_VERSION=2.1.1
-ENV PACKAGES tophat=${BOWTIE2_VERSION}*
-
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends ${PACKAGES} && \
-    apt-get clean

src/docker_modules/TopHat/2.1.1/docker_init.sh

-#!/bin/sh
-docker build src/docker_modules/TopHat/2.1.1 -t 'tophat:2.1.1'

src/docker_modules/Trimmomatic/0.36/docker_init.sh

-#!/bin/sh
-docker build src/docker_modules/Trimmomatic/0.36 -t 'trimmomatic:0.36'

src/docker_modules/UrQt/d62c1f8/docker_init.sh

-#!/bin/sh
-docker build src/docker_modules/UrQt/d62c1f8 -t 'urqt:d62c1f8'

src/docker_modules/bcftools/1.7/docker_init.sh

-#!/bin/sh
-docker build src/docker_modules/bcftools/1.7 -t 'bcftools:1.7'

src/docker_modules/bioawk/1.0/docker_init.sh

-#!/bin/sh
-docker build src/docker_modules/bioawk/1.0 -t 'bioawk:1.0'

src/docker_modules/canu/1.6/docker_init.sh

-#!/bin/sh
-docker build src/docker_modules/canu/1.6 -t 'canu:1.6'

src/docker_modules/cutadapt/1.14/docker_init.sh

-#!/bin/sh
-docker build src/docker_modules/cutadapt/1.14 -t 'cutadapt:1.14'

src/docker_modules/deepTools/3.0.2/docker_init.sh

-#!/bin/sh
-docker build src/docker_modules/deepTools/3.0.2 -t 'deeptools:3.0.2'

src/docker_modules/deepTools/3.1.1/docker_init.sh

-#!/bin/sh
-docker build src/docker_modules/deepTools/3.1.1 -t 'deeptools:3.1.1'

src/docker_modules/file_handle/0.1.1/docker_init.sh

-#!/bin/sh
-docker build src/docker_modules/file_handle/0.1.1 -t 'file_handle:0.1.1'

src/docker_modules/picard/2.18.11/docker_init.sh

-#!/bin/sh
-docker build src/docker_modules/picard/2.18.11 -t 'picard:2.18.11'

src/docker_modules/pigz/2.4/docker_init.sh

-#!/bin/sh
-docker build src/docker_modules/pigz/2.4 -t 'pigz:2.4'

src/docker_modules/sambamba/0.6.7/docker_init.sh

-#!/bin/sh
-docker build src/docker_modules/sambamba/0.6.7 -t 'sambamba:0.6.7'

src/docker_modules/samblaster/0.1.24/docker_init.sh

-#!/bin/sh
-docker build src/docker_modules/samblaster/0.1.24 -t 'samblaster:0.1.24'

src/docker_modules/ucsc/375/docker_init.sh

-#!/bin/sh
-docker build src/docker_modules/ucsc/375/ -t 'ucsc:375'

src/example_chipseq.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'
+
+workflow csv_parsing {
+  if (params.csv_path.size() > 0) {
+    log.info "loading local csv files"
+    Channel
+      .fromPath(params.csv_path, checkIfExists: true)
+      .ifEmpty { error 
+      log.error """
+    =============================================================
+      WARNING! No csv input file precised.
+      Use '--csv_path <file.csv>'
+      Or '--help' for more informations
+    =============================================================
+    """
+      }
+      .splitCsv(header: true, sep: ";", strip: true)
+      .flatMap{
+        it -> [
+          [(it.IP + it.WCE).md5(), "IP", "w", file(it.IP)],
+          [(it.IP + it.WCE).md5(), "WCE", "w", file(it.WCE)]
+        ]
+      }
+      .map{ it ->
+        if (it[1] instanceof List){
+          it
+        } else {
+          [it[0], [it[1]], it[2], it[3], [it[4]]]
+        }
+      }
+      .map{
+        it ->
+        if (it[1].size() == 2){ // if data are paired_end
+          [
+            "index": it[0],
+            "group": ref_order(it),
+            "ip": it[2],
+            "type": it[3],
+            "id": read_order(it)[0],
+            "file": read_order(it)
+          ]
+        } else {
+          [
+            "index": it[0],
+            "group": it[1].simpleName,
+            "ip": it[2],
+            "type": it[3],
+            "id": it[4].simpleName,
+            "file": [it[4].simpleName, it[4]]
+          ]
+        }
+      }
+      .set{input_csv}
+  } else {
+    log.info "loading remotes SRA csv files"
+    Channel
+      .fromPath(params.csv_sra, checkIfExists: true)
+      .ifEmpty { error 
+      log.error """
+    =============================================================
+      WARNING! No csv input file precised.
+      Use '--csv_path <file.csv>' or
+      Use '--csv_SRA <file.csv>'
+      Or '--help' for more informations
+    =============================================================
+    """
+      }
+      .splitCsv(header: true, sep: ";", strip: true)
+      .flatMap{
+        it -> [
+          [[it.IP_w + it.WCE_w + it.IP_m + it.WCE_m], t.IP_w, "IP", "w", it.IP_w],
+          [[it.IP_w + it.WCE_w + it.IP_m + it.WCE_m], it.IP_w, "WCE", "w", it.WCE_w],
+          [[it.IP_w + it.WCE_w + it.IP_m + it.WCE_m], it.IP_w, "IP", "m", it.IP_m],
+          [[it.IP_w + it.WCE_w + it.IP_m + it.WCE_m], it.IP_w, "WCE", "m", it.WCE_m]
+        ]
+      }
+      .map{
+        it ->
+        if (it[1].size() == 2){ // if data are paired_end
+          [
+            "index": (
+              it[0][0][0].simpleName +
+              it[0][0][1].simpleName +
+              it[0][0][2].simpleName +
+              it[0][0][3].simpleName
+            ).md5(),
+            "group": it[1][0].simpleName,
+            "ip": it[2],
+            "type": it[3],
+            "id": it[4][0].simpleName[0..-4],
+            "file": [it[4][0].simpleName[0..-4], it[4]]
+          ]
+        } else {
+          [
+            "index": (
+              it[0][0].simpleName +
+              it[0][1].simpleName +
+              it[0][2].simpleName +
+              it[0][3].simpleName
+            ).md5(),
+            "group": it[1].simpleName,
+            "ip": it[2],
+            "type": it[3],
+            "id": it[4].simpleName,
+            "file": [it[4].simpleName, it[4]]
+          ]
+        }
+      }
+      .set{input_csv}
+  }
+  emit:
+  input_csv
+}
+
+
+workflow {
+
+}
\ No newline at end of file

src/example_marseq.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
+nextflow.enable.dsl=2
+
+/*
+Testing pipeline for marseq scRNASeq analysis
+*/
+
+include { adaptor_removal} from "./nf_modules/cutadapt/main.nf"
+include {
+  index_fasta;
+  count;
+  index_fasta_velocity;
+  count_velocity
+} from "./nf_modules/kb/main.nf" addParams(
+  kb_protocol: "marsseq",
+  count_out: "quantification/",
+  count_velocity_out: "quantification_velocity/"
+)
+
+params.fasta = "http://ftp.ensembl.org/pub/release-98/fasta/gallus_gallus/dna/Gallus_gallus.GRCg6a.dna.toplevel.fa.gz"
+params.fastq = "data/CF42_45/*/*R{1,2}.fastq.gz"
+params.gtf = "http://ftp.ensembl.org/pub/release-98/gtf/gallus_gallus/Gallus_gallus.GRCg6a.98.gtf.gz"
+params.transcript_to_gene = ""
+params.whitelist = "data/expected_whitelist.txt"
+params.config = "data/marseq_flexi_splitter.yaml"
+params.workflow_type = "classic"
+
+log.info "fastq files (--fastq): ${params.fastq}"
+log.info "fasta file (--fasta): ${params.fasta}"
+log.info "gtf file (--gtf): ${params.gtf}"
+log.info "transcript_to_gene file (--transcript_to_gene): ${params.transcript_to_gene}"
+log.info "whitelist file (--whitelist): ${params.whitelist}"
+log.info "config file (--config): ${params.config}"
+
+channel
+  .fromFilePairs( params.fastq, size: -1)
+  .set { fastq_files }
+channel
+  .fromPath( params.fasta )
+  .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
+  .map { it -> [it.simpleName, it]}
+  .set { fasta_files }
+channel
+  .fromPath( params.gtf )
+  .ifEmpty { error "Cannot find any gtf files matching: ${params.gtf}" }
+  .map { it -> [it.simpleName, it]}
+  .set { gtf_files }
+if (params.whitelist == "") {
+  channel.empty()
+    .set { whitelist_files }
+} else {
+  channel
+    .fromPath( params.whitelist )
+    .map { it -> [it.simpleName, it]}
+    .set { whitelist_files }
+}
+channel
+  .fromPath( params.config )
+  .ifEmpty { error "Cannot find any config files matching: ${params.config}" }
+  .map { it -> [it.simpleName, it]}
+  .set { config_files }
+
+workflow {
+  adaptor_removal(fastq_files)
+  if (params.workflow_type == "classic") {
+    index_fasta(
+      fasta_files,
+      gtf_files
+    )
+    count(
+      index_fasta.out.index,
+      adaptor_removal.out.fastq,
+      index_fasta.out.t2g, whitelist_files,config_files
+    )
+  } else {
+    index_fasta_velocity(
+      fasta_files,
+      gtf_files
+    )
+    count_velocity(
+      index_fasta_velocity.out.index,
+      adaptor_removal.out.fastq,
+      index_fasta_velocity.out.t2g,
+      whitelist_files,
+      config_files
+    )
+  }
+}