Merge pull request #1507 from merszym/eager-metaphlan-update

merszym · web-flow · commit 2862660118ff · 2025-02-28T12:02:57.000+01:00
Add Metaphlan test-dataset (WIP nf-core/eager#1085)
diff --git a/README.md b/README.md
@@ -39,6 +39,8 @@ This contains two paired end samples which are the default test samples.
 
 Already clipped, merged and mapped BAM files of the two paired-end FASTQ files as described above in `fastq`.
 
+For metaphlan-tests: A BAM file TOYMETAPHLAN that contains the Mammoth fastq-files (see above) + the sequences used to construct the Metaphlan test database
+
 **vcf**
 
 `JK2772_*`: An additional VCF for another Mammoth MT capture library that was previously processed in nf-core/eager and genotyped via UnifiedGenotyper (~10K reads after merging, [Fellows Yates 2017 et al._Sci. Rep._](https://doi.org/10.1038/s41598-017-17723-1))
diff --git a/testdata/Mammoth/bam/Mammoth_MT_Krause_TOYMETAPHLAN.bam b/testdata/Mammoth/bam/Mammoth_MT_Krause_TOYMETAPHLAN.bam
diff --git a/testdata/Mammoth/samplesheet_v3_TOYMETAPHLAN.csv b/testdata/Mammoth/samplesheet_v3_TOYMETAPHLAN.csv
@@ -0,0 +1,2 @@
+sample_id,library_id,lane,colour_chemistry,pairment,strandedness,damage_treatment,r1,r2,bam,bam_reference_id
+JK2782_METAPHLAN,JK2782_TGGCCGATCAACGA_BAM,8,4,single,double,half,,,https://github.com/nf-core/test-datasets/raw/eager/testdata/Mammoth/bam/Mammoth_MT_Krause_TOYMETAPHLAN.bam,Mammoth_MT_Krause

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,2 @@`
	`1`	`+sample_id,library_id,lane,colour_chemistry,pairment,strandedness,damage_treatment,r1,r2,bam,bam_reference_id`
	`2`	`+JK2782_METAPHLAN,JK2782_TGGCCGATCAACGA_BAM,8,4,single,double,half,,,https://github.com/nf-core/test-datasets/raw/eager/testdata/Mammoth/bam/Mammoth_MT_Krause_TOYMETAPHLAN.bam,Mammoth_MT_Krause`