nf-core · Gabriel-A-Barrett · Dec 12, 2022 · Jan 25, 2023 · Jan 25, 2023 · Jan 25, 2023
diff --git 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
@@ -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
@@ -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
@@ -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
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_00.1.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_00.1.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_00.2.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_00.2.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_01.1.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_01.1.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_01.2.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_01.2.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_02.1.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_02.1.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_02.2.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_02.2.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_03.1.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_03.1.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_03.2.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_03.2.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_04.1.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_04.1.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_04.2.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_04.2.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_05.1.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_05.1.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_05.2.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_05.2.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_06.1.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_06.1.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_06.2.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_06.2.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_07.1.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_07.1.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_07.2.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_07.2.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_08.1.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_08.1.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_08.2.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_08.2.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_09.1.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_09.1.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_09.2.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_09.2.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_10.1.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_10.1.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_10.2.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_10.2.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_11.1.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_11.1.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_11.2.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_11.2.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_12.1.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_12.1.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_12.2.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_12.2.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_13.1.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_13.1.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_13.2.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_13.2.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_14.1.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_14.1.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_14.2.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_14.2.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_15.1.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_15.1.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_15.2.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_15.2.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_16.1.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_16.1.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_16.2.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_16.2.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_17.1.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_17.1.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_17.2.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_17.2.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_18.1.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_18.1.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_18.2.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_18.2.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_19.1.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_19.1.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_19.2.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci/msp_19.2.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/hsc_Chr26.fasta.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/hsc_Chr26.fasta.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_0.1.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_0.1.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_0.2.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_0.2.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_1.1.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_1.1.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_1.2.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_1.2.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_2.1.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_2.1.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_2.2.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_2.2.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_3.1.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_3.1.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_3.2.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_3.2.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_4.1.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_4.1.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_4.2.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_4.2.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_5.1.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_5.1.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_5.2.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_5.2.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_6.1.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_6.1.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_6.2.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_6.2.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_7.1.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_7.1.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_7.2.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_7.2.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_8.1.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_8.1.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_8.2.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_8.2.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_9.1.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_9.1.fq.gz
diff --git a/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_9.2.fq.gz b/testdata/Lpolyphemus/ddrad_sbfi_mluci_chr26/msp_9.2.fq.gz
diff --git a/PRJNA386062/SRR5567681/SRR5567681_1.fastq.gz → ...NA386062/SRR5567681/SRR5567681_1.fastq.gz b/PRJNA386062/SRR5567681/SRR5567681_1.fastq.gz → ...NA386062/SRR5567681/SRR5567681_1.fastq.gz
diff --git a/PRJNA386062/SRR5567681/SRR5567681_2.fastq.gz → ...NA386062/SRR5567681/SRR5567681_2.fastq.gz b/PRJNA386062/SRR5567681/SRR5567681_2.fastq.gz → ...NA386062/SRR5567681/SRR5567681_2.fastq.gz
diff --git a/PRJNA386062/SRR5567682/SRR5567682_1.fastq.gz → ...NA386062/SRR5567682/SRR5567682_1.fastq.gz b/PRJNA386062/SRR5567682/SRR5567682_1.fastq.gz → ...NA386062/SRR5567682/SRR5567682_1.fastq.gz
diff --git a/PRJNA386062/SRR5567682/SRR5567682_2.fastq.gz → ...NA386062/SRR5567682/SRR5567682_2.fastq.gz b/PRJNA386062/SRR5567682/SRR5567682_2.fastq.gz → ...NA386062/SRR5567682/SRR5567682_2.fastq.gz