Add stub blocks to all local modules

CHANGELOG.md

@@ -190,6 +190,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #148](https://github.com/nf-core/fetchngs/pull/148) - Fix default metadata fields for ENA API v2.0
 - [PR #150](https://github.com/nf-core/fetchngs/pull/150) - Add infrastructure and CI for multi-cloud full-sized tests run via Nextflow Tower
 - [PR #157](https://github.com/nf-core/fetchngs/pull/157) - Add `public_aws_ecr.config` to source mulled containers when using `public.ecr.aws` Docker Biocontainer registry
+- [PR #368](https://github.com/nf-core/fetchngs/pull/XXX) - Add stub blocks to all local modules
 
 ### Software dependencies
 

modules/local/aspera_cli/main.nf

@@ -55,4 +55,19 @@ process ASPERA_CLI {
         md5sum -c ${meta.id}_2.fastq.gz.md5
         """
     }
+
+    stub:
+    if (meta.single_end) {
+        """
+        echo "" | gzip > ${meta.id}.fastq.gz
+        touch ${meta.id}.fastq.gz.md5
+        """
+    } else {
+        """
+        echo "" | gzip > ${meta.id}_1.fastq.gz
+        echo "" | gzip > ${meta.id}_2.fastq.gz
+        touch ${meta.id}_1.fastq.gz.md5
+        touch ${meta.id}_2.fastq.gz.md5
+        """
+    }
 }

modules/local/multiqc_mappings_config/main.nf

@@ -19,4 +19,9 @@ process MULTIQC_MAPPINGS_CONFIG {
         $csv \\
         multiqc_config.yml
     """
+
+    stub:
+    """
+    touch multiqc_config.yml
+    """
 }

modules/local/sra_fastq_ftp/main.nf

@@ -48,4 +48,19 @@ process SRA_FASTQ_FTP {
         md5sum -c ${meta.id}_2.fastq.gz.md5
 """
     }
+
+    stub:
+    if (meta.single_end) {
+        """
+        echo "" | gzip > ${meta.id}.fastq.gz
+        touch ${meta.id}.fastq.gz.md5
+        """
+    } else {
+        """
+        echo "" | gzip > ${meta.id}_1.fastq.gz
+        echo "" | gzip > ${meta.id}_2.fastq.gz
+        touch ${meta.id}_1.fastq.gz.md5
+        touch ${meta.id}_2.fastq.gz.md5
+        """
+    }
 }

modules/local/sra_ids_to_runinfo/main.nf

@@ -25,4 +25,9 @@ process SRA_IDS_TO_RUNINFO {
         ${id}.runinfo.tsv \\
         $metadata_fields
     """
+
+    stub:
+    """
+    touch ${id}.runinfo.tsv
+    """
 }

modules/local/sra_runinfo_to_ftp/main.nf

@@ -19,4 +19,9 @@ process SRA_RUNINFO_TO_FTP {
         ${runinfo.join(',')} \\
         ${runinfo.toString().tokenize(".")[0]}.runinfo_ftp.tsv
     """
+
+    stub:
+    """
+    touch ${runinfo.toString().tokenize(".")[0]}.runinfo_ftp.tsv
+    """
 }

modules/local/sra_to_samplesheet/main.nf

@@ -72,4 +72,10 @@ process SRA_TO_SAMPLESHEET {
     // Write mappings to file
     def mappings_file = task.workDir.resolve("${meta.id}.mappings.csv")
     mappings_file.text = mappings
+
+    stub:
+    """
+    touch ${meta.id}.samplesheet.csv
+    touch ${meta.id}.mappings.csv
+    """
 }

workflows/fetchngs.nf

@@ -60,6 +60,7 @@ workflow FETCHNGS {
     SRA_RUNINFO_TO_FTP
         .out
         .tsv
+        .filter { it.size() > 0 }
         .splitCsv(header:true, sep:'\t')
         .map {
             meta ->