Rscript integration

conf/modules.config

@@ -12,6 +12,8 @@
 
 process {
 
+
+
     publishDir = [
         path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
         mode: params.publish_dir_mode,
@@ -45,4 +47,66 @@ process {
 	ext.args2 = 'ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True LEADING:3 TRAILING:3 MINLEN:36'
     }
 
+
+    //
+    // Alignment options
+    //
+
+
+
+
+
+
+    //
+    // Picard MarkDuplicates and Filtering options
+    //
+
+    withName: '.*BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES' {
+        ext.args   = '--ASSUME_SORTED true --REMOVE_DUPLICATES true --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp'
+        ext.prefix = { "${meta.id}.md" }
+        publishDir = [
+            [
+                path: { "${params.outdir}/reports/markduplicates" },
+                mode: params.publish_dir_mode,
+                pattern: '*metrics.txt',
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ],
+            [
+                path: { "${params.outdir}/markduplicates/bam" },
+                mode: params.publish_dir_mode,
+                pattern: '*.md.{bam,bai}',
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+                //enable: params.save_markduplicates_bam
+            ]
+        ]
+    }
+
+    withName: '.*BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX' {
+        ext.prefix  = { "${meta.id}.markdup.sorted" }
+        publishDir  = [
+            path: { "${params.outdir}/markduplicates/bam" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            pattern: '*.{bai,csi}'
+        ]
+    }
+
+    withName: '.*BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS.*' {
+        ext.args    = ""
+        publishDir  = [
+            path: { "${params.outdir}/reports/samtools_stats/${meta.id}/md/" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            pattern: '*.{stats,flagstat,idxstats}'
+        ]
+    }
+
+
+
+
+
+
+
+
+
 }

modules.json

@@ -8,13 +8,23 @@
                     "bwa/aln": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": ["fastq_align_bwaaln", "modules"]
                     },
                     "bwa/index": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
+                    "bwa/sampe": {
+                        "branch": "master",
+                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
+                        "installed_by": ["fastq_align_bwaaln"]
+                    },
+                    "bwa/samse": {
+                        "branch": "master",
+                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
+                        "installed_by": ["fastq_align_bwaaln"]
+                    },
                     "cat/fastq": {
                         "branch": "master",
                         "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
@@ -25,6 +35,11 @@
                         "git_sha": "76cc4938c1f6ea5c7d83fed1eeffc146787f9543",
                         "installed_by": ["modules"]
                     },
+                    "deeptools/bamcoverage": {
+                        "branch": "master",
+                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
+                        "installed_by": ["modules"]
+                    },
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
@@ -40,6 +55,36 @@
                         "git_sha": "f2d63bd5b68925f98f572eed70993d205cc694b7",
                         "installed_by": ["modules"]
                     },
+                    "picard/markduplicates": {
+                        "branch": "master",
+                        "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
+                        "installed_by": ["bam_markduplicates_picard", "modules"]
+                    },
+                    "samtools/faidx": {
+                        "branch": "master",
+                        "git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe",
+                        "installed_by": ["modules"]
+                    },
+                    "samtools/flagstat": {
+                        "branch": "master",
+                        "git_sha": "570ec5bcfe19c49e16c9ca35a7a116563af6cc1c",
+                        "installed_by": ["bam_stats_samtools"]
+                    },
+                    "samtools/idxstats": {
+                        "branch": "master",
+                        "git_sha": "e662ab16e0c11f1e62983e21de9871f59371a639",
+                        "installed_by": ["bam_stats_samtools"]
+                    },
+                    "samtools/index": {
+                        "branch": "master",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "installed_by": ["bam_markduplicates_picard", "fastq_align_bwaaln"]
+                    },
+                    "samtools/stats": {
+                        "branch": "master",
+                        "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
+                        "installed_by": ["bam_stats_samtools"]
+                    },
                     "trimmomatic": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
@@ -51,6 +96,25 @@
                         "installed_by": ["modules"]
                     }
                 }
+            },
+            "subworkflows": {
+                "nf-core": {
+                    "bam_markduplicates_picard": {
+                        "branch": "master",
+                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
+                        "installed_by": ["subworkflows"]
+                    },
+                    "bam_stats_samtools": {
+                        "branch": "master",
+                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
+                        "installed_by": ["bam_markduplicates_picard"]
+                    },
+                    "fastq_align_bwaaln": {
+                        "branch": "master",
+                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
+                        "installed_by": ["subworkflows"]
+                    }
+                }
             }
         }
     }

modules/local/chromosomes_size.nf

@@ -0,0 +1,16 @@
+process CUT_SIZES_GENOME {
+    tag "${sample_id}"
+    publishDir "${params.outdir}/genome", mode: 'copy'
+
+    input:
+    tuple val(meta), path(fai)
+
+    output:
+    path("sizes.genome") , emit: ch_sizes_genome
+
+    script:
+    """
+    cut -f1,2 ${fai} > sizes.genome
+    """
+}
+

modules/local/rtwosamplesmle/main.nf

@@ -0,0 +1,100 @@
+// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
+//               https://github.com/nf-core/modules/tree/master/modules/nf-core/
+//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
+//               https://nf-co.re/join
+// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
+//               All other parameters MUST be provided using the "task.ext" directive, see here:
+//               https://www.nextflow.io/docs/latest/process.html#ext
+//               where "task.ext" is a string.
+//               Any parameters that need to be evaluated in the context of a particular sample
+//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
+// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
+//               unless there is a run-time, storage advantage in implementing in this way
+//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
+//                 bwa mem | samtools view -B -T ref.fasta
+// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
+//               list (`[]`) instead of a file can be used to work around this issue.
+
+process RTWOSAMPLESMLE {
+    //tag "$meta.id"
+    label 'process_medium'
+
+    // TODO nf-core: List required Conda package(s).
+    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
+    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
+    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
+
+    //conda "YOUR-TOOL-HERE"
+
+    //container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+    //   'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE':
+    //   'biocontainers/YOUR-TOOL-HERE' }"
+
+    //docker pull lucidif/r_two_samples_mle:0.0.1
+    //docker image tag ae028b17f7d3 quay.io/lucidif/r_two_samples_mle:0.0.1
+    //container 'lucidif/r_two_samples_mle:0.0.1'
+    //container 'https://registry-1.docker.io/v2/lucidif/r_two_samples_mle/blobs/sha256:038e9a5189bd7f946bc85db99ea5c43cce8b643c4e3723d52a2a763b8cf21304'
+
+    input:
+    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
+    //               MUST be provided as an input via a Groovy Map called "meta".
+    //               This information may not be required in some instances e.g. indexing reference genome files:
+    //               https://github.com/nf-core/modules/blob/master/modules/nf-core/bwa/index/main.nf
+    // TODO nf-core: Where applicable please provide/convert compressed files as input/output
+    //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
+    //tuple val(meta1), val(meta2), path(bam1), path(bam2)
+    tuple val(meta), path(bam1), path(bam2)
+    path chromsizes_file
+
+
+    //output:
+    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
+    //tuple val(meta), path("*.bam"), emit: bam
+    // TODO nf-core: List additional required output channels/values here
+    //path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+
+    //def args = task.ext.args ?: ''
+    //def prefix = task.ext.prefix ?: "${meta.id}"
+
+    // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
+    //               If the software is unable to output a version number on the command-line then it can be manually specified
+    //               e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/homer/annotatepeaks/main.nf
+    //               Each software used MUST provide the software name and version number in the YAML version file (versions.yml)
+    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
+    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
+    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
+    // TODO nf-core: Please replace the example samtools command below with your module's command
+    // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
+
+
+
+    //    bam_list_ch
+    //         .map { it[0].collate(2) } // Raggruppa ogni due elementi
+    //         .set { paired_bam_list_ch }        
+
+
+    template 'two_samples_mle.R'
+
+    //stub:
+
+    //def args = task.ext.args ?: ''
+    //def prefix = task.ext.prefix ?: "${meta.id}"
+
+    // TODO nf-core: A stub section should mimic the execution of the original module as best as possible
+    //               Have a look at the following examples:
+    //               Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63
+    //               Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54
+    // """
+    // touch ${prefix}.bam
+
+    // cat <<-END_VERSIONS > versions.yml
+    // "${task.process}":
+    //     : \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ))
+    // END_VERSIONS
+    // """
+}