diff --git a/README.md b/README.md index 639fcc2a3..187e2aca5 100644 --- a/README.md +++ b/README.md @@ -1,16 +1,23 @@ -# ![nfcore/test-datasets](docs/images/test-datasets_logo.png) -Test data to be used for automated testing with the nf-core pipelines +# test-datasets: `radseq` -## Introduction +This branch contains test data for [nf-core/radseq](blah) pipeline -nf-core is a collection of high quality Nextflow pipelines. +## Content of this repository -## Documentation -nf-core/test-datasets comes with documentation in the `docs/` directory: +`testdata/PRJNA386062`: ezRAD sequences from... -01. [Add a new test dataset](https://github.com/nf-core/test-datasets/blob/master/docs/ADD_NEW_DATA.md) -02. [Use an existing test dataset](https://github.com/nf-core/test-datasets/blob/master/docs/USE_EXISTING_DATA.md) +### For Reference Based Approach Or Denovo + +#### Simulated Horseshoe Crab Data + +`testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/hsc_Chr26.fasta` chromosome 26 of Atlantic Horseshoe Crab + +`testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_[0..9].{1,2}.fq.gz` simulated ddRAD reads + +`testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/popmap.txt` id and corresponding population + +`samplesheet/samplesheet_test_lpolyphemus_ddrad_sbfi_mluci_chr26.csv` input sample sheet for this dataset ## Support -For further information or help, don't hesitate to get in touch on our [Gitter channel](https://gitter.im/nf-core/Lobby) +For further information or help, don't hesitate to get in touch on our [Slack `#radseq` channel](https://nfcore.slack.com/channels/radseq) (you can join with [this invite](https://nf-co.re/join/slack)). diff --git a/samplesheet/samplesheet_test_SRR5567681.csv b/samplesheet/samplesheet_test_SRR5567681.csv new file mode 100644 index 000000000..09532d4be --- /dev/null +++ b/samplesheet/samplesheet_test_SRR5567681.csv @@ -0,0 +1,3 @@ +sample,fastq_1,fastq_2,umi_barcodes +SRR5567681,testdata/PRJNA386062/SRR5567681/SRR5567681_1.fastq.gz,testdata/PRJNA386062/SRR5567681/SRR5567681_2.fastq.gz,FALSE +SRR5567682,testdata/PRJNA386062/SRR5567682/SRR5567682_1.fastq.gz,testdata/PRJNA386062/SRR5567682/SRR5567682_2.fastq.gz,FALSE diff --git a/samplesheet/samplesheet_test_lpolyphemus_ddrad_sbfi_mluci.csv b/samplesheet/samplesheet_test_lpolyphemus_ddrad_sbfi_mluci.csv new file mode 100644 index 000000000..b33dcbd67 --- /dev/null +++ b/samplesheet/samplesheet_test_lpolyphemus_ddrad_sbfi_mluci.csv @@ -0,0 +1,5 @@ +sample,fastq_1,fastq_2,umi_barcodes +msp_00,https://raw.githubusercontent.com/Gabriel-A-Barrett/test-datasets/radseq/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_00.1.fq.gz,https://raw.githubusercontent.com/Gabriel-A-Barrett/test-datasets/radseq/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_00.2.fq.gz,false +msp_01,https://raw.githubusercontent.com/Gabriel-A-Barrett/test-datasets/radseq/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_01.1.fq.gz,https://raw.githubusercontent.com/Gabriel-A-Barrett/test-datasets/radseq/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_01.2.fq.gz,false +msp_02,https://raw.githubusercontent.com/Gabriel-A-Barrett/test-datasets/radseq/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_02.1.fq.gz,https://raw.githubusercontent.com/Gabriel-A-Barrett/test-datasets/radseq/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_02.2.fq.gz,false +msp_03,https://raw.githubusercontent.com/Gabriel-A-Barrett/test-datasets/radseq/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_03.1.fq.gz,https://raw.githubusercontent.com/Gabriel-A-Barrett/test-datasets/radseq/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_03.2.fq.gz,false diff --git a/samplesheet/samplesheet_test_lpolyphemus_ddrad_sbfi_mluci_chr26.csv b/samplesheet/samplesheet_test_lpolyphemus_ddrad_sbfi_mluci_chr26.csv new file mode 100644 index 000000000..5f9011b69 --- /dev/null +++ b/samplesheet/samplesheet_test_lpolyphemus_ddrad_sbfi_mluci_chr26.csv @@ -0,0 +1,11 @@ +sample,fastq_1,fastq_2,umi_barcodes +msp_0,https://raw.githubusercontent.com/Gabriel-A-Barrett/test-datasets/radseq/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_0.1.fq.gz,https://raw.githubusercontent.com/Gabriel-A-Barrett/test-datasets/radseq/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_0.2.fq.gz,false +msp_1,https://raw.githubusercontent.com/Gabriel-A-Barrett/test-datasets/radseq/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_1.1.fq.gz,https://raw.githubusercontent.com/Gabriel-A-Barrett/test-datasets/radseq/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_1.2.fq.gz,false +msp_2,https://raw.githubusercontent.com/Gabriel-A-Barrett/test-datasets/radseq/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_2.1.fq.gz,https://raw.githubusercontent.com/Gabriel-A-Barrett/test-datasets/radseq/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_2.2.fq.gz,false +msp_3,https://raw.githubusercontent.com/Gabriel-A-Barrett/test-datasets/radseq/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_3.1.fq.gz,https://raw.githubusercontent.com/Gabriel-A-Barrett/test-datasets/radseq/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_3.2.fq.gz,false +msp_4,https://raw.githubusercontent.com/Gabriel-A-Barrett/test-datasets/radseq/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_4.1.fq.gz,https://raw.githubusercontent.com/Gabriel-A-Barrett/test-datasets/radseq/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_4.2.fq.gz,false +msp_5,https://raw.githubusercontent.com/Gabriel-A-Barrett/test-datasets/radseq/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_5.1.fq.gz,https://raw.githubusercontent.com/Gabriel-A-Barrett/test-datasets/radseq/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_5.2.fq.gz,false +msp_6,https://raw.githubusercontent.com/Gabriel-A-Barrett/test-datasets/radseq/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_6.1.fq.gz,https://raw.githubusercontent.com/Gabriel-A-Barrett/test-datasets/radseq/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_6.2.fq.gz,false +msp_7,https://raw.githubusercontent.com/Gabriel-A-Barrett/test-datasets/radseq/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_7.1.fq.gz,https://raw.githubusercontent.com/Gabriel-A-Barrett/test-datasets/radseq/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_7.2.fq.gz,false +msp_8,https://raw.githubusercontent.com/Gabriel-A-Barrett/test-datasets/radseq/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_8.1.fq.gz,https://raw.githubusercontent.com/Gabriel-A-Barrett/test-datasets/radseq/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_8.2.fq.gz,false +msp_9,https://raw.githubusercontent.com/Gabriel-A-Barrett/test-datasets/radseq/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_9.1.fq.gz,https://raw.githubusercontent.com/Gabriel-A-Barrett/test-datasets/radseq/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_9.2.fq.gz,false diff --git a/testdata/Lpolyphemus/Chr1.fa.gz b/testdata/Lpolyphemus/Chr1.fa.gz new file mode 100644 index 000000000..7eab30b55 Binary files /dev/null and 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