Coda workflow

assets/schema_tools.json

@@ -0,0 +1,61 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema",
+    "title": "nf-core/differentialabundance - params.tools schema",
+    "description": "Schema for the file provided with params.tools",
+    "type": "array",
+    "items": {
+        "type": "object",
+        "properties": {
+            "pathway_name": {
+                "type": "string",
+                "meta": ["pathway_name"]
+            },
+            "diff_method": {
+                "type": "string",
+                "errorMessage": "choose propd, DESeq2 or none",
+                "meta": ["diff_method"]
+            },
+            "args_diff": {
+                "type": "string",
+                "meta": ["args_diff"]
+            },
+            "enr_diff_method": {
+                "type": "string",
+                "meta": ["enr_diff_method"],
+                "errorMessage": "choose grea, gsea or none"
+            },
+            "args_enr_diff": {
+                "type": "string",
+                "meta": ["args_enr_diff"]
+            },
+            "cor_method": {
+                "type": "string",
+                "meta": ["cor_method"],
+                "errorMessage": "choose correlation,proportionality, partial correlation or none"
+            },
+            "args_cor": {
+                "type": "string",
+                "meta": ["args_cor"]
+            },
+            "enr_cor_method": {
+                "type": "string",
+                "meta": ["enr_cor_method"],
+                "errorMessage": "choose grea or none"
+            },
+            "args_enr_cor": {
+                "type": "string",
+                "meta": ["args_enr_cor"]
+            },
+            "sel_method": {
+                "type": "string",
+                "meta": ["sel_method"],
+                "errorMessage": "choose filtervar or none"
+            },
+            "args_sel": {
+                "type": "string",
+                "meta": ["args_sel"]
+            }
+        },
+        "required": []
+    }
+}

assets/tools_samplesheet.csv

@@ -0,0 +1,6 @@
+pathway_name,diff_method,args_diff,enr_diff_method,args_enr_diff,cor_method,args_cor,enr_cor_method,args_enr_cor,sel_method,args_sel
+diff_prop,propd, --adjacency true --permutation 100 --fixseed true, , ,,, , ,,
+filtered_pcor,propd, --adjacency true --permutation 100 --fixseed true, , ,propr,  --permutation 10 --adjacency true --cutoff_min 0.005 --cutoff_max 0.5 --cutoff_interval 0.01 --metric pcor.bshrink, , , filtervar,
+prop,, , , ,propr,  --cutoff_min 0.05 --cutoff_max 0.95 --cutoff_interval 0.05 --fixseed true --metric rho --permutation 100 --adjacency true, , , ,
+diff_grea,propd,--group_col fase --adjacency true --permutation 10,grea, --permutation 10, , , , ,,
+deseq2,deseq2,,gsea,,,,,,,

conf/crg.config

@@ -0,0 +1,41 @@
+params {
+    config_profile_name = 'CRG profile'
+    config_profile_description = 'Configuration to run on CRG cluster'
+
+    max_cpus = 64
+    max_memory = 100.GB
+    max_time   = 48.h
+}
+
+
+process {
+    executor = 'crg'
+    //maxRetries = params.max_retries
+    //errorStrategy = params.err_start
+
+    withLabel:process_low {
+        queue = 'cn-el7,short-centos79'
+        cpus   = { check_max( 2                  , 'cpus'    ) }
+        memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
+    }
+    withLabel:process_medium{
+        queue = 'cn-el7,short-centos79'
+        cpus   = { check_max( 6                  , 'cpus'    ) }
+        memory = { check_max( 36.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 8.h  * task.attempt, 'time'    ) }
+    }
+    withLabel:process_high {
+        queue = 'cn-el7,long-centos79'
+        cpus   = { check_max( 12                  , 'cpus'    ) }
+        memory = { check_max( 56.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 12.h  * task.attempt, 'time'    ) }
+
+    }
+}
+
+
+singularity {
+    enabled  = true
+    cacheDir = 'singularity_cache'
+}

conf/modules_coda.config

@@ -0,0 +1,45 @@
+process {
+    withName: "PROPR"{
+        ext.args = { "${meta.args_cor}" == "null" ? '' : "${meta.args_cor}" }
+        publishDir = [
+            path: { "${params.outdir}/correlation_analysis/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+    withName: "PROPD"{
+        ext.args = { "${meta.args_diff}" == "null" ? '' : "${meta.args_diff}" }
+        publishDir = [
+            path: { "${params.outdir}/differential_analysis/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: "FILTERVAR"{
+        ext.args = { "${meta.args_cor}" == "null" ? '' : "${meta.args_cor}" }
+        publishDir = [
+            path: { "${params.outdir}/variable_selection/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: "GREA_DIFF"{
+        ext.args = { "${meta.args_enr_diff}" == "null" ? '' : "${meta.args_enr_diff}" }
+        publishDir = [
+            path: { "${params.outdir}/enrichment_differential/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: "GREA_COR"{
+        ext.args = { "${meta.args_enr_cor}" == "null" ? '' : "${meta.args_enr_cor}" }
+        publishDir = [
+            path: { "${params.outdir}/enrichment_correlation/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+}

main_coda.nf

@@ -0,0 +1,40 @@
+// include { PROPR_PROPR        } from '../../../modules/nf-core/propr/propr/main'
+// include { PROPR_PROPD        } from '../../../modules/nf-core/propr/propd/main'
+// include { PROPR_GREA         } from '../../../modules/nf-core/propr/grea/main'
+// include { MYGENE             } from '../../../modules/nf-core/mygene/main'
+include { EXPERIMENTAL        } from './subworkflows/experimental/main.nf'
+include { fromSamplesheet } from 'plugin/nf-validation'
+
+
+// These are local files from my Bachelor Thesis project, I am creating the ch_samples_and_matrix
+// manually for testing but it should be be provided by the processing section of nf-core/differentialabundance
+Counts_ch = Channel.fromPath("../YMC/counts_sin0.csv")
+
+Sample_ch = Channel.fromPath("../YMC/samplesheet_RCvsOX.csv")
+    .map{ it -> [[id: 'YMC'], it]}
+
+ch_samples_and_matrix = Sample_ch.combine(Counts_ch)
+
+// Convert the samplesheet.csv in a channel with the proper format
+ch_tools = Channel.fromSamplesheet('tools')
+
+
+// TO DO: This should be modified to run one path per default, not all
+if (params.pathway == "all") {
+    ch_tools
+        .set{ ch_tools_single }
+} else {
+    ch_tools
+        .filter{
+            it[0]["pathway_name"] == params.pathway // TO DO: change pathway to path also in the tools_samplesheet file
+        }
+        //.view()
+        .set{ ch_tools_single }
+}
+ch_tools_single.view()
+
+workflow {
+    EXPERIMENTAL(ch_samples_and_matrix, ch_tools_single)
+    EXPERIMENTAL.out.output.view()
+}
+

modules.json

@@ -60,6 +60,26 @@
                         "git_sha": "9326d73af3fbe2ee90d9ce0a737461a727c5118e",
                         "installed_by": ["modules"]
                     },
+                    "mygene": {
+                        "branch": "master",
+                        "git_sha": "82024cf6325d2ee194e7f056d841ecad2f6856e9",
+                        "installed_by": ["modules"]
+                    },
+                    "propr/grea": {
+                        "branch": "master",
+                        "git_sha": "71b1180a5a3de6398eb0eb4d55424cbda36f52d8",
+                        "installed_by": ["modules"]
+                    },
+                    "propr/propd": {
+                        "branch": "master",
+                        "git_sha": "08b360512467e8e7079f995bb7c981a7c204d00f",
+                        "installed_by": ["modules"]
+                    },
+                    "propr/propr": {
+                        "branch": "master",
+                        "git_sha": "132fa6c9bd2515807f6a1cdec1ad7d03c817bcc9",
+                        "installed_by": ["modules"]
+                    },
                     "proteus/readproteingroups": {
                         "branch": "master",
                         "git_sha": "a069b29783583c219c1f23ed3dcf64a5aee1340b",

modules/local/filtervar/main.nf

@@ -0,0 +1,23 @@
+process FILTERVAR {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/r-propr:5.0.3':
+        'quay.io/biocontainers/r-propr:5.0.3' }"
+
+    input:
+    tuple val(meta), path(count), path(adj_matrix)
+
+    output:
+    tuple val(meta), path("*.count_filtered.tsv"),  emit: count
+    path "*.R_sessionInfo.log",                     emit: session_info
+    path "versions.yml",                            emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    template 'filtervar.R'
+}