From da3d2d96e6f04ee382ac63888fe1fbb2497d5abc Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Fri, 9 Dec 2022 10:27:50 +0100
Subject: [PATCH] Fix linting

---
 README.md    |   2 +-
 modules.json | 117 ++++++++++++++++++++++++++++++++++-----------------
 2 files changed, 79 insertions(+), 40 deletions(-)

diff --git a/README.md b/README.md
index 767fceb..3f45cba 100644
--- a/README.md
+++ b/README.md
@@ -54,7 +54,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 ## Quick Start
 
-1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`).
+1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`).
 
 2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_.
 
diff --git a/modules.json b/modules.json
index fe1c8ac..377e902 100644
--- a/modules.json
+++ b/modules.json
@@ -7,35 +7,43 @@
                 "nf-core": {
                     "adapterremoval": {
                         "branch": "master",
-                        "git_sha": "ce7cf27e377fdacf7ebe8e75903ec70405ea1659"
+                        "git_sha": "ce7cf27e377fdacf7ebe8e75903ec70405ea1659",
+                        "installed_by": ["modules"]
                     },
                     "bbmap/bbduk": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "bowtie2/align": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "bowtie2/build": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "bracken/bracken": {
                         "branch": "master",
-                        "git_sha": "8cab56516076b23c6f8eb1ac20ba4ce9692c85e1"
+                        "git_sha": "8cab56516076b23c6f8eb1ac20ba4ce9692c85e1",
+                        "installed_by": ["modules"]
                     },
                     "cat/fastq": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "centrifuge/centrifuge": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "centrifuge/kreport": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
@@ -44,23 +52,28 @@
                     },
                     "diamond/blastx": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "eido/convert": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "eido/validate": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "falco": {
                         "branch": "master",
-                        "git_sha": "fc959214036403ad83efe7a41d43d0606c445cda"
+                        "git_sha": "fc959214036403ad83efe7a41d43d0606c445cda",
+                        "installed_by": ["modules"]
                     },
                     "fastp": {
                         "branch": "master",
-                        "git_sha": "1e49f31e93c56a3832833eef90a02d3cde5a3f7e"
+                        "git_sha": "1e49f31e93c56a3832833eef90a02d3cde5a3f7e",
+                        "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
@@ -69,79 +82,98 @@
                     },
                     "filtlong": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "kaiju/kaiju": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "kaiju/kaiju2krona": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "kaiju/kaiju2table": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "kraken2/kraken2": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "krakentools/combinekreports": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "krakentools/kreport2krona": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "krakenuniq/preloadedkrakenuniq": {
                         "branch": "master",
-                        "git_sha": "05649975c6611c6e007537a7984e186e12ae03af"
+                        "git_sha": "05649975c6611c6e007537a7984e186e12ae03af",
+                        "installed_by": ["modules"]
                     },
                     "krona/ktimporttaxonomy": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "krona/ktimporttext": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "malt/run": {
                         "branch": "master",
-                        "git_sha": "6d9712f03ec2de8264a50ee4541a617e1e063b51"
+                        "git_sha": "6d9712f03ec2de8264a50ee4541a617e1e063b51",
+                        "installed_by": ["modules"]
                     },
                     "megan/rma2info": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "metaphlan3/mergemetaphlantables": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "metaphlan3/metaphlan3": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "minimap2/align": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "minimap2/index": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "motus/merge": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "motus/profile": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
@@ -150,31 +182,38 @@
                     },
                     "porechop/porechop": {
                         "branch": "master",
-                        "git_sha": "2a4e85eb81875a572bb58133e37f84ba3cc484d7"
+                        "git_sha": "2a4e85eb81875a572bb58133e37f84ba3cc484d7",
+                        "installed_by": ["modules"]
                     },
                     "prinseqplusplus": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "samtools/bam2fq": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "samtools/view": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "installed_by": ["modules"]
                     }
                 }
             }