From c7e62dd7db3fad93aa918c88cceff36fb0a71d6a Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 31 Mar 2022 18:01:29 +0100 Subject: [PATCH 1/6] Update CHANGELOG after merging template updates --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 56f5432d..a8d65c7c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Enhancements & fixes +- Updated pipeline template to [nf-core/tools 2.3.2](https://github.com/nf-core/tools/releases/tag/2.3.2) + ### Parameters ## [[2.4.1](https://github.com/nf-core/viralrecon/releases/tag/2.4.1)] - 2022-03-01 From 5fa21911c890307b73531d1dda640fdae408cc56 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 31 Mar 2022 22:15:22 +0100 Subject: [PATCH 2/6] Fix template merge bug --- subworkflows/local/input_check.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf index 35f79aac..9d83d9f1 100644 --- a/subworkflows/local/input_check.nf +++ b/subworkflows/local/input_check.nf @@ -21,7 +21,7 @@ workflow INPUT_CHECK { .out .csv .splitCsv ( header:true, sep:',' ) - .map { create_fastq_channels(it) } + .map { create_fastq_channel(it) } .set { sample_info } } else if (platform == 'nanopore') { SAMPLESHEET_CHECK From bd19710be76c837513395fe46b8e1430683a4a8f Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Fri, 1 Apr 2022 11:14:36 +0100 Subject: [PATCH 3/6] Remove TODO statement in README --- README.md | 63 ++++++++++++++++++++++++++++++++++++++++++++++++++----- 1 file changed, 58 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 8aa66dc3..dbc0a07d 100644 --- a/README.md +++ b/README.md @@ -99,11 +99,64 @@ A number of improvements were made to the pipeline recently, mainly with regard 4. Start running your own analysis! - - - ```console - nextflow run nf-core/viralrecon --input samplesheet.csv --outdir --genome GRCh37 -profile - ``` + - Typical command for Illumina shotgun analysis: + + ```bash + nextflow run nf-core/viralrecon \ + --input samplesheet.csv \ + --outdir \ + --platform illumina \ + --protocol metagenomic \ + --genome 'MN908947.3' \ + -profile + ``` + + - Typical command for Illumina amplicon analysis: + + ```bash + nextflow run nf-core/viralrecon \ + --input samplesheet.csv \ + --outdir \ + --platform illumina \ + --protocol amplicon \ + --genome 'MN908947.3' \ + --primer_set artic \ + --primer_set_version 3 \ + --skip_assembly \ + -profile + ``` + + - Typical command for Nanopore amplicon analysis: + + ```bash + nextflow run nf-core/viralrecon \ + --input samplesheet.csv \ + --outdir \ + --platform nanopore \ + --genome 'MN908947.3' \ + --primer_set_version 3 \ + --fastq_dir fastq_pass/ \ + --fast5_dir fast5_pass/ \ + --sequencing_summary sequencing_summary.txt \ + -profile + ``` + + - An executable Python script called [`fastq_dir_to_samplesheet.py`](https://github.com/nf-core/viralrecon/blob/master/bin/fastq_dir_to_samplesheet.py) has been provided if you are using `--platform illumina` and would like to auto-create an input samplesheet based on a directory containing FastQ files **before** you run the pipeline (requires Python 3 installed locally) e.g. + + ```console + wget -L https://raw.githubusercontent.com/nf-core/viralrecon/master/bin/fastq_dir_to_samplesheet.py + ./fastq_dir_to_samplesheet.py samplesheet.csv + ``` + + - You can find the default keys used to specify `--genome` in the [genomes config file](https://github.com/nf-core/configs/blob/master/conf/pipeline/viralrecon/genomes.config). This provides default options for + + - Reference genomes (including SARS-CoV-2) + - Genome associates primer sets + - [Nextclade datasets](https://docs.nextstrain.org/projects/nextclade/en/latest/user/datasets.html) + + The Pangolin and Nextclade lineage and clade definitions change regularly as new SARS-CoV-2 lineages are discovered. For instructions to use more recent versions of lineage analysis tools like Pangolin and Nextclade please refer to the [updating containers](https://nf-co.re/viralrecon/usage#updating-containers) section in the usage docs. + + Where possible we are trying to collate links and settings for standard primer sets to make it easier to run the pipeline with standard keys; see [usage docs](https://nf-co.re/viralrecon/usage#illumina-primer-sets). ## Documentation From 952d10af7763502f3e8be16b510a2527eee8efcd Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Fri, 1 Apr 2022 11:16:20 +0100 Subject: [PATCH 4/6] Remove retry logic from AWS actions --- .github/workflows/awsfulltest.yml | 3 --- .github/workflows/awstest.yml | 3 --- 2 files changed, 6 deletions(-) diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 3135180c..5600fcf9 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -29,6 +29,3 @@ jobs: "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/viralrecon/results-${{ github.sha }}/platform_${{ matrix.platform }}" } profiles: test_full_${{ matrix.platform }},aws_tower - nextflow_config: | - process.errorStrategy = 'retry' - process.maxRetries = 3 diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index f9631c28..a3ce4a0a 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -23,6 +23,3 @@ jobs: "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/viralrecon/results-test-${{ github.sha }}" } profiles: test,aws_tower - nextflow_config: | - process.errorStrategy = 'retry' - process.maxRetries = 3 From 3d5c5605d88d6349f0ea13932b61986d6d16adea Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Fri, 1 Apr 2022 11:21:19 +0100 Subject: [PATCH 5/6] Add .prettierignore file --- .prettierignore | 8 ++++++++ 1 file changed, 8 insertions(+) create mode 100644 .prettierignore diff --git a/.prettierignore b/.prettierignore new file mode 100644 index 00000000..37a8f6aa --- /dev/null +++ b/.prettierignore @@ -0,0 +1,8 @@ +.nextflow* +work/ +data/ +results/ +.DS_Store +testing/ +testing* +*.pyc \ No newline at end of file From 408b31eb90683a1025245f4f46c36d2e00fbf402 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Fri, 1 Apr 2022 11:43:49 +0100 Subject: [PATCH 6/6] Fix ECLint --- .prettierignore | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.prettierignore b/.prettierignore index 37a8f6aa..5124c9ac 100644 --- a/.prettierignore +++ b/.prettierignore @@ -5,4 +5,4 @@ results/ .DS_Store testing/ testing* -*.pyc \ No newline at end of file +*.pyc