From e2b0a7cc210447a556dd5c824f12f45513149c4e Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 8 Jan 2024 13:07:28 +0000 Subject: [PATCH 1/4] [automated] Fix linting with Prettier --- README.md | 3 --- 1 file changed, 3 deletions(-) diff --git a/README.md b/README.md index c8bf525..fed07df 100644 --- a/README.md +++ b/README.md @@ -35,7 +35,6 @@ ## Usage - > [!NOTE] > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. @@ -66,12 +65,10 @@ nextflow run nf-core/detaxizer \ --outdir ``` - > [!WARNING] > Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; > see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). - For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/detaxizer/usage) and the [parameter documentation](https://nf-co.re/detaxizer/parameters). ## Pipeline output From 5aa6e599e349ecaf8aba1c75c7336411dd7f720a Mon Sep 17 00:00:00 2001 From: Jannik Seidel <127119345+jannikseidelQBiC@users.noreply.github.com> Date: Mon, 8 Jan 2024 14:56:21 +0100 Subject: [PATCH 2/4] fixed main.nf of dumpsoftwareversion --- modules/nf-core/custom/dumpsoftwareversions/main.nf | 2 -- 1 file changed, 2 deletions(-) diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index 645c271..7685b33 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -7,8 +7,6 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { 'https://depot.galaxyproject.org/singularity/multiqc:1.17--pyhdfd78af_0' : 'biocontainers/multiqc:1.17--pyhdfd78af_0' }" - - input: path versions From a302b85f8d027a89798abd1086212f604695659b Mon Sep 17 00:00:00 2001 From: Jannik Seidel <127119345+jannikseidelQBiC@users.noreply.github.com> Date: Mon, 8 Jan 2024 14:58:43 +0100 Subject: [PATCH 3/4] fixed main.nf of fastqc --- modules/nf-core/fastqc/main.nf | 2 -- 1 file changed, 2 deletions(-) diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 8450418..9e19a74 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -7,8 +7,6 @@ process FASTQC { 'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' : 'biocontainers/fastqc:0.12.1--hdfd78af_0' }" - - input: tuple val(meta), path(reads) From 2f501bd484331bc5702ba47da314d06647074c3f Mon Sep 17 00:00:00 2001 From: Jannik Seidel <127119345+jannikseidelQBiC@users.noreply.github.com> Date: Mon, 8 Jan 2024 15:02:12 +0100 Subject: [PATCH 4/4] fixed multiqc_config.yml --- assets/multiqc_config.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 8e3eede..96fb15e 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,6 +1,4 @@ report_comment: > - - This report has been generated by the nf-core/detaxizer analysis pipeline. For information about how to interpret these results, please see the documentation.