Merge pull request #63 from nf-core/feature/nf-core_subworkflows

Workflow updates

CHANGELOG.md

@@ -3,6 +3,19 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v1.1.0dev
+
+### `Added`
+
+- [#63](https://github.com/nf-core/demultiplex/pull/63) Replace local bcl_demultiplex subworkflow with nf-core version
+- [#63](https://github.com/nf-core/demultiplex/pull/63) Add bases_demultiplex local subworkflow
+- [#63](https://github.com/nf-core/demultiplex/pull/63) Replace fastqc with falco for speedier QC, fixes Replace fastqc with falco #62
+- [#64](https://github.com/nf-core/demultiplex/pull/64) Add subway map by @nvnieuwk
+
+### `Fixed`
+
+- [#63](https://github.com/nf-core/demultiplex/pull/63) Fix MultiQC report inputs, fixes MultiQC report is empty #64
+
 ## v1.0.0 - 2022-10-06
 
 Initial release of nf-core/demultiplex, created with the [nf-core](https://nf-co.re/) template.

CITATIONS.md

@@ -14,7 +14,7 @@
 
   > Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018 Sep 1;34(17):i884-i890. doi: 10.1093/bioinformatics/bty560. PubMed PMID: 30423086; PubMed Central PMCID: PMC6129281.
 
-- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+- [Falco](https://github.com/smithlabcode/falco)
 
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 

README.md

@@ -29,7 +29,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
 - [bcl2fastq](#bcl2fastq) - converting bcl files to fastq, and demultiplexing (CONDITIONAL)
 
 2. [fastp](#fastp) - Adapter and quality trimming
-3. [FastQC](#fastqc) - Raw read QC
+3. [Falco](#falco) - Raw read QC
 4. [md5sum](#md5sum) - Creates an MD5 (128-bit) checksum of every fastq.
 5. [MultiQC](#multiqc) - aggregate report, describing results of the whole pipeline
 

assets/multiqc_config.yml

@@ -11,3 +11,6 @@ report_section_order:
     order: -1002
 
 export_plots: true
+sp:
+  fastqc/data:
+    fn: "*_fastqc_data.txt"

conf/modules.config

@@ -25,7 +25,6 @@ process {
     }
 
     withName: BCLCONVERT {
-        ext.when = { params.demultiplexer == "bclconvert" }
         ext.args = {[
             meta.lane ? "--bcl-only-lane ${meta.lane}" : "",
             "--force",
@@ -62,7 +61,6 @@ process {
     }
 
     withName: BCL2FASTQ {
-        ext.when = { params.demultiplexer == "bcl2fastq" }
         ext.args = {[
             meta.lane ? "--tiles s_${meta.lane}" : "",
         ].join(" ").trim()}
@@ -97,7 +95,6 @@ process {
     }
 
     withName: CELLRANGER_MKFASTQ {
-        ext.when = { params.demultiplexer == "cellranger" }
         publishDir = [
             path: { "${params.outdir}/fastq" },
             mode: params.publish_dir_mode,
@@ -106,7 +103,6 @@ process {
     }
 
     withName: BASES2FASTQ {
-        ext.when = { params.demultiplexer == "bases2fastq" }
         ext.args = "--strict"
         publishDir = [
             [
@@ -138,7 +134,7 @@ process {
         ]
     }
 
-    withName: FASTQC {
+    withName: FALCO {
         publishDir = [
             path: { "${params.outdir}/${meta.fcid}" },
             mode: params.publish_dir_mode,

docs/output.md

@@ -14,7 +14,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - [bases2fastq](#bases2fastq) - converting bases files to fastq, and demultiplexing (CONDITIONAL)
 - [bcl2fastq](#bcl2fastq) - converting bcl files to fastq, and demultiplexing (CONDITIONAL)
 - [fastp](#fastp) - Adapter and quality trimming
-- [FastQC](#fastqc) - Raw read QC
+- [Falco](#falco) - Raw read QC
 - [md5sum](#md5sum) - Creates an MD5 (128-bit) checksum of every fastq.
 - [MultiQC](#multiqc) - aggregate report, describing results of the whole pipeline
 
@@ -72,20 +72,21 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 ![MultiQC - fastp filtered reads plot](images/mqc_fastp_plot.png)
 
-### FastQC
+### Falco
 
 <details markdown="1">
 <summary>Output files</summary>
 
 - `<flowcell_id>/`
   - `*_fastqc.html`: FastQC report containing quality metrics.
-  - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images.
+  - `*_fastqc.txt`: Txt containing the FastQC report, tab-delimited data file.
+  - `*_summary.txt`: Txt containing the summary metrics.
 
-> **NB:** The FastQC plots in this directory are generated relative to the raw, input reads. They may contain adapter sequence and regions of low quality. To see how your reads look after adapter and quality trimming please refer to the FastQC reports in the `trimgalore/fastqc/` directory.
+> **NB:** The FastQC plots in this directory are generated relative to the raw, demultiplexed reads. They may contain adapter sequence and regions of low quality.
 
 </details>
 
-[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
+[Falco](https://github.com/smithlabcode/falco) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences.
 
 ![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png)
 

lib/FormattingService.groovy

@@ -0,0 +1,59 @@
+/**
+ * MIT License
+ *
+ * Copyright (c) 2022 Moritz E. Beber
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in all
+ * copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ */
+
+import static groovy.json.JsonOutput.prettyPrint
+import groovy.json.JsonGenerator
+import java.nio.file.Path
+import java.time.OffsetDateTime
+import nextflow.util.Duration
+
+/**
+ * Define a service that formats objects for printing.
+ *
+ * @author Moritz E. Beber
+ */
+class FormattingService {
+
+    /**
+    * Define a JSON generator with appropriate converters for problematic types.
+    */
+    protected static JsonGenerator generator = new JsonGenerator.Options()
+        .dateFormat("yyyy-MM-dd'T'HH:mm:ssXXX")
+        .addConverter(OffsetDateTime) { OffsetDateTime offset -> offset.toString() }
+        .addConverter(Duration) { Duration duration -> duration.toString() }
+        .addConverter(Path) { Path filename -> filename.toString() }
+        .build()
+
+    /**
+    * Create a pretty string format of a given object using JSON.
+    *
+    * @param object The given object (typically a map) that is to be represented as a
+    *     JSON-like pretty string.
+    * @return A JSON string.
+    */
+    static String prettyFormat(Object object) {
+        return prettyPrint(generator.toJson(object))
+    }
+
+}

modules.json

@@ -7,7 +7,7 @@
                 "nf-core": {
                     "bases2fastq": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "f67b13d71bad1a1d805283b9537449141dff384e"
                     },
                     "bcl2fastq": {
                         "branch": "master",
@@ -21,11 +21,11 @@
                         "branch": "master",
                         "git_sha": "8022c68e7403eecbd8ba9c49496f69f8c49d50f0"
                     },
-                    "fastp": {
+                    "falco": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "fc959214036403ad83efe7a41d43d0606c445cda"
                     },
-                    "fastqc": {
+                    "fastp": {
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
@@ -42,6 +42,14 @@
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     }
                 }
+            },
+            "subworkflows": {
+                "nf-core": {
+                    "bcl_demultiplex": {
+                        "branch": "master",
+                        "git_sha": "cc980fb6f3931cb02fbae41ebd0cece34c7638f4"
+                    }
+                }
             }
         }
     }