Merge pull request #127 from agrima2010/alignment_tools

Added alignment tools - bwamem index and mem

Author: agrima2010

conf/modules.config

@@ -35,6 +35,21 @@ process {
         ]
     }
 
+    withName: 'BWAMEM2_INDEX' {
+        publishDir = [
+            path: { "${params.outdir}/bwamem2_index" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+    withName: 'BWAMEM2_MEM' {
+        publishDir = [
+            path: { "${params.outdir}/bwamem2_mem" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: 'MULTIQC_GLOBAL' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [

conf/test.config

@@ -10,14 +10,6 @@
 ----------------------------------------------------------------------------------------
 */
 
-process {
-    resourceLimits = [
-        cpus: 4,
-        memory: '15.GB',
-        time: '1.h'
-    ]
-}
-
 params {
     config_profile_name        = 'Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
@@ -31,3 +23,13 @@ params {
     // Genome references
     genome = 'R64-1-1'
 }
+
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+
+}
+

main.nf

@@ -7,29 +7,24 @@
     Website: https://nf-co.re/seqinspector
     Slack  : https://nfcore.slack.com/channels/seqinspector
 ----------------------------------------------------------------------------------------
-*/
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
+    GENOME PARAMETER VALUES
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { SEQINSPECTOR            } from './workflows/seqinspector'
-include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
-include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
-include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
+params.fasta = getGenomeAttribute('fasta')
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    GENOME PARAMETER VALUES
+    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-// TODO nf-core: Remove this line if you don't need a FASTA file
-//   This is an example of how to use getGenomeAttribute() to fetch parameters
-//   from igenomes.config using `--genome`
-// params.fasta = getGenomeAttribute('fasta')
+include { SEQINSPECTOR            } from './workflows/seqinspector'
+include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
+include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -50,6 +45,7 @@ workflow NFCORE_SEQINSPECTOR {
     //
     // WORKFLOW: Run pipeline
     //
+
     SEQINSPECTOR (
         samplesheet
     )
@@ -67,9 +63,12 @@ workflow NFCORE_SEQINSPECTOR {
 workflow {
 
     main:
+
+
     //
     // SUBWORKFLOW: Run initialisation tasks
     //
+
     PIPELINE_INITIALISATION (
         params.version,
         params.validate_params,
@@ -83,7 +82,7 @@ workflow {
     // WORKFLOW: Run main workflow
     //
     NFCORE_SEQINSPECTOR (
-        PIPELINE_INITIALISATION.out.samplesheet
+        PIPELINE_INITIALISATION.out.samplesheet,
     )
     //
     // SUBWORKFLOW: Run completion tasks
@@ -99,6 +98,25 @@ workflow {
     )
 }
 
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    FUNCTIONS
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+//
+// Get attribute from genome config file e.g. fasta
+//
+
+def getGenomeAttribute(attribute) {
+    if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
+        if (params.genomes[params.genome].containsKey(attribute)) {
+            return params.genomes[params.genome][attribute]
+        }
+    }
+    return null
+}
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     THE END

modules.json

@@ -10,6 +10,17 @@
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
+                    "bwamem2/index": {
+                        "branch": "master",
+                        "git_sha": "b2902040b9cb9b7b32b62400f1c024a709bd4812",
+                        "installed_by": ["modules"]
+                    },
+                    "bwamem2/mem": {
+                        "branch": "master",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/bwamem2/mem/bwamem2-mem.diff"
+                    },
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296",