fix linting

Author: mashehu

CITATION.cff

@@ -1,32 +1,6 @@
 cff-version: 1.2.0
 message: "If you use `nf-core tools` in your work, please cite the `nf-core` publication"
 authors:
-  - family-names: Ewels
-    given-names: Philip
-  - family-names: Peltzer
-    given-names: Alexander
-  - family-names: Fillinger
-    given-names: Sven
-  - family-names: Patel
-    given-names: Harshil
-  - family-names: Alneberg
-    given-names: Johannes
-  - family-names: Wilm
-    given-names: Andreas
-  - family-names: Ulysse Garcia
-    given-names: Maxime
-  - family-names: Di Tommaso
-    given-names: Paolo
-  - family-names: Nahnsen
-    given-names: Sven
-title: "The nf-core framework for community-curated bioinformatics pipelines."
-version: 2.4.1
-doi: 10.1038/s41587-020-0439-x
-date-released: 2022-05-16
-url: https://github.com/nf-core/tools
-prefered-citation:
-  type: article
-  authors:
     - family-names: Ewels
       given-names: Philip
     - family-names: Peltzer
@@ -45,12 +19,38 @@ prefered-citation:
       given-names: Paolo
     - family-names: Nahnsen
       given-names: Sven
-  doi: 10.1038/s41587-020-0439-x
-  journal: nature biotechnology
-  start: 276
-  end: 278
-  title: "The nf-core framework for community-curated bioinformatics pipelines."
-  issue: 3
-  volume: 38
-  year: 2020
-  url: https://dx.doi.org/10.1038/s41587-020-0439-x
+title: "The nf-core framework for community-curated bioinformatics pipelines."
+version: 2.4.1
+doi: 10.1038/s41587-020-0439-x
+date-released: 2022-05-16
+url: https://github.com/nf-core/tools
+prefered-citation:
+    type: article
+    authors:
+        - family-names: Ewels
+          given-names: Philip
+        - family-names: Peltzer
+          given-names: Alexander
+        - family-names: Fillinger
+          given-names: Sven
+        - family-names: Patel
+          given-names: Harshil
+        - family-names: Alneberg
+          given-names: Johannes
+        - family-names: Wilm
+          given-names: Andreas
+        - family-names: Ulysse Garcia
+          given-names: Maxime
+        - family-names: Di Tommaso
+          given-names: Paolo
+        - family-names: Nahnsen
+          given-names: Sven
+    doi: 10.1038/s41587-020-0439-x
+    journal: nature biotechnology
+    start: 276
+    end: 278
+    title: "The nf-core framework for community-curated bioinformatics pipelines."
+    issue: 3
+    volume: 38
+    year: 2020
+    url: https://dx.doi.org/10.1038/s41587-020-0439-x

README.md

@@ -114,7 +114,6 @@ Within the local clone of your fork:
 2.  **add** the documentation file to the [`docs/`](https://github.com/nf-core/configs/tree/master/docs) directory
 3.  **edit** and add your custom profile to the [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) file in the top-level directory of the clone
 4.  **add** your profile name to GitHub Actions YAML `profile:` scope (under strategy matrix) in [`.github/workflows/main.yml`](.github/workflows/main.yml).
-
     - If you forget to do this the tests will fail with the error in GitHub Actions:
 
           ```bash

conf/daisybio.config

@@ -76,6 +76,3 @@ profiles {
     }
 
 }
-
-
-

conf/embl_hd.config

@@ -42,4 +42,3 @@ executor {
     exitReadTimeout = "5 min"
     retry.reason = "*"
 }
-

conf/icr_alma.config

@@ -48,7 +48,3 @@ singularity {
     pullTimeout = 2.h
     cacheDir = '/data/scratch/shared/SINGULARITY-DOWNLOAD/nextflow/.singularity'
 }
-
-
-
-

conf/ki_luria.config

@@ -19,4 +19,3 @@ process {
     executor       = 'slurm'
     clusterOptions = '-p normal'
 }
-

conf/mssm.config

@@ -133,4 +133,3 @@ process {
     // Set default failOnMissingField behavior (optional)
     shell = ['/bin/bash', '-euo', 'pipefail']
 }
-

conf/tes.config

@@ -19,5 +19,3 @@ tes {
     basicUsername   = params.basicUsername
     basicPassword   = params.basicPassword
 }
-
-

conf/vsc_kul_uhasselt.config

@@ -316,5 +316,3 @@ profiles {
         }
     }
 }
-
-

docs/vsc_calcua.md

@@ -120,14 +120,12 @@ nextflow run nf-core/rnaseq \
 2.  Load Nextflow in your job script via the command: `module load Nextflow/23.04.2`. Alternatively, when using [your own version of Nextflow](#availability-of-nextflow), use `module load Java`.
 
 3.  Choose whether you want to use the [Slurm job scheduler to queue individual pipeline tasks](#schedule-nextflow-pipeline-using-slurm) (default mode) or if you prefer [local execution on a single node](#local-nextflow-run-on-a-single-interactive-node).
-
     - For Slurm scheduling, you only need to specify the `vsc_calcua` profile. E.g., `nextflow run pipeline -profile vsc_calcua`. Nextflow tasks will be scheduled as Slurm jobs to your current partition (or the one defined via `sbatch --partion=<partition-name>`).
     - For local execution mode on a single node, you need to append an additional sub-profile. E.g., `nextflow run pipeline -profile vsc_calcua,single_node`.
 
     Note that the `-profile` option can take multiple values, the first one always being `vsc_calcua` and the second `single_node` one being optional.
 
 4.  Specify the _partition_ that you want to run the pipeline on using the [`sbatch` command's `--partition=<name>` option](https://docs.vscentrum.be/jobs/job_submission.html#specifying-a-partition) and how many _resources_ should be allocated. See the [overview of partitions and their resources](#overview-of-partitions-and-resources) below, or refer to [the CalcUA documentation](https://docs.vscentrum.be/antwerp/tier2_hardware.html) for more info.
-
     - For the default Slurm scheduling, the partition on which the head process runs has no effect on the resources allocated to the actual pipeline tasks; these will instead be requested by Nextflow depending on the particular process' requirements and limited by the maximum thresholds set for each partition in this config.
     - For local execution mode on a single node, it is probably convenient to simply request a full node (e.g., `--cpus-per-task=28` and `--mem=112G` for broadwell), but if fewer resources are requested, these limits will be passed on the Nextflow too.
     - Omitting `--mem-per-cpu` or `--mem` will [allocate the default memory value](https://docs.vscentrum.be/jobs/job_submission.html#requesting-memory), which is the total available memory divided by the number of cores, e.g., `28 * 4 GB = 112 GB` for broadwell (`128 GB - 16 GB buffer`).