Added preprocessing subworkflow

modules.json

@@ -5,25 +5,40 @@
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
+                    "blast/blastp": {
+                        "branch": "master",
+                        "git_sha": "6330227ba2a71d39f35b0ef60e381f456489c6ee",
+                        "installed_by": [
+                            "modules"
+                        ]
+                    },
                     "falco": {
                         "branch": "master",
                         "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "fastp": {
                         "branch": "master",
                         "git_sha": "d9ec4ef289ad39b8a662a7a12be50409b11df84b",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "af27af1be706e6a2bb8fe454175b0cdf77f47b49",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     }
                 }
             },
@@ -32,20 +47,26 @@
                     "utils_nextflow_pipeline": {
                         "branch": "master",
                         "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
                         "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
                         "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     }
                 }
             }
         }
     }
-}
+}

subworkflows/local/preprocessing/main.nf

@@ -0,0 +1,58 @@
+// TODO nf-core: If in doubt look at other nf-core/subworkflows to see how we are doing things! :)
+//               https://github.com/nf-core/modules/tree/master/subworkflows
+//               You can also ask for help via your pull request or on the #subworkflows channel on the nf-core Slack workspace:
+//               https://nf-co.re/join
+// TODO nf-core: A subworkflow SHOULD import at least two modules
+
+include { FASTQC                 } from '../../../modules/nf-core/fastqc/main'
+include { FALCO                  } from '../../../modules/nf-core/falco/main'
+include { FASTP                  } from '../../../modules/nf-core/fastp/main'
+
+workflow PREPROCESSING {
+
+    take:
+    // TODO nf-core: edit input (take) channels
+    ch_samplesheet // channel: [ val(meta), [ bam ] ]
+
+    main:
+    // TODO nf-core: substitute modules here for the modules of your subworkflow
+    ch_versions = channel.empty()
+
+    //
+    // MODULE: Run FASTP
+    //
+    ch_fastp = ch_samplesheet.map { meta, reads -> tuple(meta, reads, []) }
+
+    FASTP (
+        ch_fastp,
+        [],
+        [],
+        []
+    )
+    ch_versions = ch_versions.mix( FASTP.out.versions )
+
+    //
+    // MODULE: Run FALCO
+    //
+    FALCO (
+        FASTP.out.reads
+    )
+    ch_versions = ch_versions.mix( FALCO.out.versions )
+
+    //
+    // MODULE: Run FastQC
+    //
+
+    FASTQC (
+        ch_samplesheet
+    )
+    ch_versions = ch_versions.mix( FASTQC.out.versions )
+
+    emit:
+    // TODO nf-core: edit emitted channels
+    fastqc = FASTQC.out.zip
+    versions = ch_versions
+    //bam      = SAMTOOLS_SORT.out.bam           // channel: [ val(meta), [ bam ] ]
+    //bai      = SAMTOOLS_INDEX.out.bai          // channel: [ val(meta), [ bai ] ]
+    //csi      = SAMTOOLS_INDEX.out.csi          // channel: [ val(meta), [ csi ] ]
+}

subworkflows/local/preprocessing/meta.yml

@@ -0,0 +1,51 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "preprecessing"
+## TODO nf-core: Add a description of the subworkflow and list keywords
+description: Sort SAM/BAM/CRAM file
+keywords:
+  - sort
+  - bam
+  - sam
+  - cram
+## TODO nf-core: Add a list of the modules and/or subworkflows used in the subworkflow
+components:
+  - samtools/sort
+  - samtools/index
+## TODO nf-core: List all of the channels used as input with a description and their structure
+input:
+  - ch_bam:
+      type: file
+      description: |
+        The input channel containing the BAM/CRAM/SAM files
+        Structure: [ val(meta), path(bam) ]
+      pattern: "*.{bam/cram/sam}"
+## TODO nf-core: List all of the channels used as output with a descriptions and their structure
+output:
+  - bam:
+      type: file
+      description: |
+        Channel containing BAM files
+        Structure: [ val(meta), path(bam) ]
+      pattern: "*.bam"
+  - bai:
+      type: file
+      description: |
+        Channel containing indexed BAM (BAI) files
+        Structure: [ val(meta), path(bai) ]
+      pattern: "*.bai"
+  - csi:
+      type: file
+      description: |
+        Channel containing CSI files
+        Structure: [ val(meta), path(csi) ]
+      pattern: "*.csi"
+  - versions:
+      type: file
+      description: |
+        File containing software versions
+        Structure: [ path(versions.yml) ]
+      pattern: "versions.yml"
+authors:
+  - "@FernandoDuarteF"
+maintainers:
+  - "@FernandoDuarteF"

subworkflows/local/preprocessing/tests/main.nf.test

@@ -0,0 +1,46 @@
+// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
+// nf-core subworkflows test preprecessing
+nextflow_workflow {
+
+    name "Test Subworkflow PREPRECESSING"
+    script "../main.nf"
+    workflow "PREPRECESSING"
+
+    tag "subworkflows"
+    tag "subworkflows_"
+    tag "subworkflows/preprecessing"
+    // TODO nf-core: Add tags for all modules used within this subworkflow. Example:
+    tag "samtools"
+    tag "samtools/sort"
+    tag "samtools/index"
+
+
+    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used
+    test("sarscov2 - bam - single_end") {
+
+        when {
+            workflow {
+                """
+                // TODO nf-core: define inputs of the workflow here. Example:
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                ]
+                input[1] = [
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                ]
+                """
+            }
+        }
+        then {
+            assert workflow.success
+            assertAll(
+                { assert snapshot(
+                    workflow.out
+                    //TODO nf-core: Add all required assertions to verify the test output.
+                ).match() }
+            )
+        }
+    }
+}

workflows/fsb.nf

@@ -3,7 +3,8 @@
     IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
-include { FASTQC                 } from '../modules/nf-core/fastqc/main'
+
+include { PREPROCESSING          } from '../subworkflows/local/preprocessing'
 include { MULTIQC                } from '../modules/nf-core/multiqc/main'
 include { paramsSummaryMap       } from 'plugin/nf-schema'
 include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'
@@ -24,14 +25,14 @@ workflow FSB {
 
     ch_versions = channel.empty()
     ch_multiqc_files = channel.empty()
-    //
-    // MODULE: Run FastQC
-    //
-    FASTQC (
+
+    PREPROCESSING (
         ch_samplesheet
     )
-    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]})
-    ch_versions = ch_versions.mix(FASTQC.out.versions.first())
+    ch_versions = ch_versions.mix( PREPROCESSING.out.versions )
+
+    // ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]})
+    // ch_versions = ch_versions.mix(FASTQC.out.versions.first())
 
     //
     // Collate and save software versions