add pypi release

data/get_data.py

@@ -0,0 +1,39 @@
+#!/usr/bin/env python
+
+
+import pandas as pd
+import os
+
+s3_path = "s3://bioanalyze-omics-dev/reference/nf-core/test-datasets/rnaseq/"
+df = pd.read_csv(
+    "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/v3.10/samplesheet_test.csv"
+)
+
+fastq_1s = []
+fastq_2s = []
+os.makedirs("data", exist_ok=True)
+os.chdir("data")
+for fastq_1, fastq_2 in zip(df["fastq_1"].tolist(), df["fastq_2"].tolist()):
+    if isinstance(fastq_1, str):
+        print(fastq_1)
+        if not os.path.exists(os.path.basename(fastq_1)):
+            os.system(f"wget {fastq_1}")
+        fastq_1 = os.path.basename(fastq_1)
+        os.system(f"aws s3 cp {fastq_1} {s3_path}")
+        fastq_1s.append(f"{s3_path}{fastq_1}")
+    else:
+        fastq_1s.append(None)
+
+    if isinstance(fastq_2, str):
+        print(fastq_2)
+        if not os.path.exists(os.path.basename(fastq_2)):
+            os.system(f"wget {fastq_2}")
+        fastq_2 = os.path.basename(fastq_2)
+        os.system(f"aws s3 cp {fastq_1} {s3_path}")
+        fastq_2s.append(f"{s3_path}{fastq_2}")
+    else:
+        fastq_2s.append(None)
+
+df['fastq_1'] = fastq_1s
+df['fastq_2'] = fastq_2s
+df.to_csv("samplesheet-omics.csv", index=False)

data/samplesheet_test.csv

@@ -0,0 +1,8 @@
+sample,fastq_1,fastq_2,strandedness
+WT_REP1,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357070_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357070_2.fastq.gz,auto
+WT_REP1,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357071_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357071_2.fastq.gz,auto
+WT_REP2,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357072_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357072_2.fastq.gz,reverse
+RAP1_UNINDUCED_REP1,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357073_1.fastq.gz,,reverse
+RAP1_UNINDUCED_REP2,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357074_1.fastq.gz,,reverse
+RAP1_UNINDUCED_REP2,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357075_1.fastq.gz,,reverse
+RAP1_IAA_30M_REP1,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357076_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357076_2.fastq.gz,reverse