diff --git a/.github/workflows/test_pipeline.yaml b/.github/workflows/test_pipeline.yaml index ec1154f..da25da3 100644 --- a/.github/workflows/test_pipeline.yaml +++ b/.github/workflows/test_pipeline.yaml @@ -25,14 +25,16 @@ jobs: sudo mv nextflow /usr/local/bin/ - name: Run Nextflow Illumina AQUASCOPE with Docker run: | - nextflow run main.nf --resume -profile docker,test_illumina -entry AQUASCOPE --outdir ~/testing/complete + nextflow run main.nf --resume -profile docker,test_illumina -entry AQUASCOPE --outdir ~/projects/complete - name: Set up Singularity uses: singularityhub/install-singularity@main - name: Run Nextflow Illumina QUALITY_ALIGN with Singularity - run: nextflow run main.nf --resume -profile singularity,test_illumina -entry QUALITY_ALIGN --outdir ~/testing/illumina + run: nextflow run main.nf --resume -profile singularity,test_illumina -entry QUALITY_ALIGN --outdir ~/projects/illumina/quality - name: Run Nextflow Illumina AQUASCOPE with Singularity - run: nextflow run main.nf --resume -profile singularity,test_illumina -entry AQUASCOPE --outdir ~/testing/complete - - name: Run Nextflow Illumina FREYJA_ONLY with Singularity - run: nextflow run main.nf --resume -profile singularity,test_bam -entry FREYJA_ONLY --outdir ~/testing/freyja + run: nextflow run main.nf --resume -profile singularity,test_illumina -entry AQUASCOPE --outdir ~/projects/illumina/complete + - name: Run Nextflow Illumina AQUASCOPE with Singularity + run: nextflow run main.nf --resume -profile singularity,test_bam -entry AQUASCOPE --outdir ~/projects/bam/complete + - name: Run Nextflow Ion Torrent FREYJA_ONLY with Singularity + run: nextflow run main.nf --resume -profile singularity,test_iontorrent -entry AQUASCOPE --outdir ~/projects/iontorrent/complete - name: Run Nextflow ONT AQUASCOPE with Singularity - run: nextflow run main.nf --resume -profile singularity,test_ont -entry AQUASCOPE --outdir ~/testing/ont + run: nextflow run main.nf --resume -profile singularity,test_ont -entry AQUASCOPE --outdir ~/projects/ont/complete diff --git a/VERSION b/VERSION index ad55eb8..6c8dc7e 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -v3.0.0 +v3.1.0 diff --git a/assets/samplesheet_test_iontorrent.csv b/assets/samplesheet_test_iontorrent.csv index 53ba300..19292a8 100755 --- a/assets/samplesheet_test_iontorrent.csv +++ b/assets/samplesheet_test_iontorrent.csv @@ -1,2 +1,2 @@ sample,platform,fastq_1,fastq_2,lr,bam_file,bedfile -SAMPLE1,iontorrent,,,,test/sample1.bam,https://raw.githubusercontent.com/artic-network/primer-schemes/master/nCoV-2019/V3/nCoV-2019.primer.bed +SAMPLE1,iontorrent,,,,test/Sample1.bam,https://raw.githubusercontent.com/artic-network/primer-schemes/master/nCoV-2019/V3/nCoV-2019.primer.bed diff --git a/docs/user-guide/preparing-files.md b/docs/user-guide/preparing-files.md index 258d4f6..ccd868a 100755 --- a/docs/user-guide/preparing-files.md +++ b/docs/user-guide/preparing-files.md @@ -16,7 +16,9 @@ You will need to create a samplesheet with information about the samples you wou - [Ion-torrent example](https://github.com/CDCgov/aquascope/blob/main/assets/samplesheet_test_iontorrent.csv) Notes: + - Currently, Illumina, Ion-torrent and Oxford Nanopore platforms are supported in this pipeline. + - Bedfiles can be a local file path or a raw.github url The pipeline will auto-detect whether a sample is single- or paired-end using the information provided in the samplesheet. It auto-detects sequencing platform (Illumina, Ion-torrent and Oxford nanopore) and determines which set of tools have to be run. The samplesheet must have 7 columns, and have to be in the same order as the header shown below. @@ -32,7 +34,7 @@ SAMPLE1_SE,illumina,https://raw.githubusercontent.com/nf-core/test-datasets/vira | Column | Description | illumina | nanopore | iontorrent | |----------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------------|--------------|---------------------| | `sample` | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). | Required | Required | Required | -| `platform` | Sequencing platform. This entry will determine the type of sequencing used. It is an important entry as the decision to run a set of tools is determined by this entry. | Required | Required | Required | +| `platform` | Sequencing platform. This entry will determine the type of sequencing used. It is an important entry as the decision to run a set of tools is determined by this entry. (Accepted entrys: "illumina", "nanopore", "iontorrent") | Required | Required | Required | | `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | Required | NA | NA | | `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | Required | NA | NA | | `lr` | Full path to FastQ file for ONT long reads. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". fast5 files are not expected or accepted | NA | Required | NA | @@ -42,6 +44,17 @@ SAMPLE1_SE,illumina,https://raw.githubusercontent.com/nf-core/test-datasets/vira ## Samplesheet for `FREYJA_ONLY` workflow +Option 1. Create a samplesheet using the following reference: + + - [BAM example](../../assets/samplesheet_test_bam.csv) + +Option 2. Create samplesheet for primer trimmed bams using the python script `bin/bam_to_samplesheet.py` + ``` + python bin/bam_to_samplesheet.py \ + --directory \ + --output " + ``` + ```console sample,bam_file Sample1,test/Sample1.bam @@ -54,18 +67,7 @@ Sample2,test/Sample2.bam | `bam_file` | Full path to BAM file for Ion-torrent short reads. File has to .bam strictly| -Option 1. Create a samplesheet using the following reference: - - [BAM example](../../assets/samplesheet_test_bam.csv) - -Option 2. Create samplesheet for primer trimmed bams using the python script `bin/bam_to_samplesheet.py` - ``` - python bin/bam_to_samplesheet.py \ - --directory \ - --output " - ``` - ## Prepare the config files -Prepare the configuration files A. `scicomp.config`: CDC specific config to run on SciComp resources. diff --git a/docs/user-guide/test-info.md b/docs/user-guide/test-info.md index 7fc1002..f9e5a2d 100755 --- a/docs/user-guide/test-info.md +++ b/docs/user-guide/test-info.md @@ -21,13 +21,13 @@ Test [samplesheet](https://github.com/CDCgov/aquascope/blob/dev/assets/sampleshe ### CDC Internal Users nextflow run \ main.nf \ --profile test_illumina,singularity,scicomp_rosalind +-profile test_illumina,singularity,scicomp_rosalind \ -entry AQUASCOPE ### All Other Users nextflow run \ main.nf \ --profile test_illumina, \ -entry AQUASCOPE ``` @@ -38,13 +38,13 @@ Test [samplesheet](https://github.com/CDCgov/aquascope/blob/dev/assets/sampleshe ### CDC Internal Users nextflow run \ main.nf \ --profile test_ont,singularity,scicomp_rosalind +-profile test_ont,singularity,scicomp_rosalind \ -entry AQUASCOPE ### All Other Users nextflow run \ main.nf \ --profile test_ont, \ -entry AQUASCOPE ``` @@ -55,13 +55,13 @@ Test [samplesheet](https://github.com/CDCgov/aquascope/blob/main/assets/samplesh ### CDC Internal Users nextflow run \ main.nf \ --profile test_bams,singularity,scicomp_rosalind +-profile test_bams,singularity,scicomp_rosalind \ -entry AQUASCOPE ### All Other Users nextflow run \ main.nf \ --profile test_bams, \ -entry AQUASCOPE ``` D. Test Iontorrent Input @@ -71,13 +71,13 @@ Test [samplesheet](https://github.com/CDCgov/aquascope/blob/dev/assets/sampleshe ### CDC Internal Users nextflow run \ main.nf \ --profile test_iontorrent,singularity,scicomp_rosalind +-profile test_iontorrent,singularity,scicomp_rosalind \ -entry AQUASCOPE ### All Other Users nextflow run \ main.nf \ --profile test_iontorrent, \ -entry AQUASCOPE ```