1
0
Fork 0
mirror of https://github.com/MillironX/taxprofiler.git synced 2024-11-25 00:39:54 +00:00

Fix linting

This commit is contained in:
James Fellows Yates 2022-12-09 10:27:50 +01:00
parent 1ccd0a0767
commit da3d2d96e6
2 changed files with 79 additions and 40 deletions

View file

@ -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))_.

View file

@ -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"]
}
}
}