Merge pull request #7 from DLBPointon/clearing

Removing unnecessary code

README.md

@@ -2,7 +2,6 @@
 
 [![GitHub Actions CI Status](https://github.com/nf-core/treeval/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/treeval/actions?query=workflow%3A%22nf-core+CI%22)
 [![GitHub Actions Linting Status](https://github.com/nf-core/treeval/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/treeval/actions?query=workflow%3A%22nf-core+linting%22)
-[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?logo=Amazon%20AWS)](https://nf-co.re/treeval/results)
 [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8)](https://doi.org/10.5281/zenodo.XXXXXXX)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/)
@@ -11,9 +10,6 @@
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg)](https://sylabs.io/docs/)
 [![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/treeval)
 
-[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23treeval-4A154B?logo=slack)](https://nfcore.slack.com/channels/treeval)
-[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?logo=twitter)](https://twitter.com/nf_core)
-[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?logo=youtube)](https://www.youtube.com/c/nf-core)
 
 ## Introduction
 
@@ -25,14 +21,11 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 
 <!-- TODO nf-core: Add full-sized test dataset and amend the paragraph below if applicable -->
 
-On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/treeval/results).
-
 ## Pipeline summary
 
 <!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
 
-1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+
 
 ## Quick Start
 
@@ -67,7 +60,7 @@ The nf-core/treeval pipeline comes with documentation about the pipeline [usage]
 
 ## Credits
 
-nf-core/treeval was originally written by Damon-Lee Pointon, Yumi Sims, William Eagles.
+nf-core/treeval was originally written by Damon-Lee Pointon, Yumi Sims and William Eagles.
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 

modules.json

@@ -15,14 +15,8 @@
             "diamond/blastx": {
                 "git_sha": "bd3bfe0817246082525ab93707976676b1fe208b"
             },
-            "fastqc": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
-            },
             "minimap2/align": {
                 "git_sha": "1a5a9e7b4009dcf34e6867dd1a5a1d9a718b027b"
-            },
-            "multiqc": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             }
         }
     }

workflows/treeval.nf

@@ -18,15 +18,7 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true
 if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
 
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    CONFIG FILES
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
 
-ch_multiqc_config        = file("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
-ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
-
-/*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     IMPORT LOCAL MODULES/SUBWORKFLOWS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -46,8 +38,7 @@ include { INPUT_CHECK } from '../subworkflows/local/input_check'
 //
 // MODULE: Installed directly from nf-core/modules
 //
-include { FASTQC                      } from '../modules/nf-core/modules/fastqc/main'
-include { MULTIQC                     } from '../modules/nf-core/modules/multiqc/main'
+
 include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main'
 
 /*
@@ -71,36 +62,11 @@ workflow TREEVAL {
     )
     ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)
 
-    //
-    // MODULE: Run FastQC
-    //
-    FASTQC (
-        INPUT_CHECK.out.reads
-    )
-    ch_versions = ch_versions.mix(FASTQC.out.versions.first())
 
     CUSTOM_DUMPSOFTWAREVERSIONS (
         ch_versions.unique().collectFile(name: 'collated_versions.yml')
     )
 
-    //
-    // MODULE: MultiQC
-    //
-    workflow_summary    = WorkflowTreeval.paramsSummaryMultiqc(workflow, summary_params)
-    ch_workflow_summary = Channel.value(workflow_summary)
-
-    ch_multiqc_files = Channel.empty()
-    ch_multiqc_files = ch_multiqc_files.mix(Channel.from(ch_multiqc_config))
-    ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_custom_config.collect().ifEmpty([]))
-    ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
-    ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
-    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
-
-    MULTIQC (
-        ch_multiqc_files.collect()
-    )
-    multiqc_report = MULTIQC.out.report.toList()
-    ch_versions    = ch_versions.mix(MULTIQC.out.versions)
 }
 
 /*