[WIP] Large dataset test branch

.circleci/config.yml

@@ -134,6 +134,8 @@ variables:
           source activate lcdb-wf-test
           ./run_test.sh --use-conda -j2 -k -p -r
           python chipseq_trackhub.py config/config.yaml config/hub_config.yaml
+          source activate lcdb-wf-test-r
+          Rscript -e "rmarkdown::render('downstream/diffbind.Rmd')"
   # --------------------------------------------------------------------------
   # Previous versions had an error where chipseq peaks needed to be defined for
   # every caller. This does a (relatively) quick test to only run a single
@@ -268,7 +270,7 @@ variables:
 
           # test PE reads
           ./run_test.sh -j 2 --use-conda -k -p -r --until multiqc \
-            --configfile $ORIG/test/test_configs/override.yaml \
+            --configfile $ORIG/test/test_configs/override_PE.yaml \
             --config sampletable=$ORIG/test/test_configs/test_pe_sampletable.tsv
 
 

.gitignore

@@ -11,6 +11,11 @@ workflows/rnaseq/downstream/upset_plots
 workflows/rnaseq/downstream/final_clusters
 workflows/rnaseq/downstream/rnaseq.log
 workflows/rnaseq/downstream/*tsv
+workflows/chipseq/downstream/diffbind.html
+workflows/chipseq/downstream/diffbind_cache
+workflows/chipseq/downstream/diffbind_files
+workflows/chipseq/downstream/*tsv
+workflows/chipseq/downstream/*bed
 workflows/chipseq/data
 workflows/rnaseq/data
 workflows/colocalization/results

ci/get-data.py

@@ -6,9 +6,10 @@
 shell.executable('/bin/bash')
 BRANCH = 'master'
 URL = 'https://github.com/lcdb/lcdb-test-data/blob/{0}/data/{{}}?raw=true'.format(BRANCH)
+URLH = 'https://github.com/lcdb/lcdb-test-data-human/blob/{0}/{{}}?raw=true'.format(BRANCH)
 
 
-def _download_file(fn, dest=None):
+def _download_file(URL, fn, dest=None):
     url = URL.format(fn)
     if dest is None:
         dest = fn
@@ -17,21 +18,61 @@ def _download_file(fn, dest=None):
     shell('wget -q -O- {url} > {dest}')
     return dest
 
+_download_file(URLH, 'rnaseq_samples/A549_DMSO_1h_1/A549_DMSO_1h_1.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/A549_DMSO_1h_1.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/A549_DMSO_1h_2/A549_DMSO_1h_2.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/A549_DMSO_1h_2.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/A549_DMSO_6h_1/A549_DMSO_6h_1.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/A549_DMSO_6h_1.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/A549_DMSO_6h_2/A549_DMSO_6h_2.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/A549_DMSO_6h_2.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/A549_JQ1_1h_1/A549_JQ1_1h_1.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/A549_JQ1_1h_1.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/A549_JQ1_1h_2/A549_JQ1_1h_2.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/A549_JQ1_1h_2.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/A549_JQ1_6h_1/A549_JQ1_6h_1.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/A549_JQ1_6h_1.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/A549_JQ1_6h_2/A549_JQ1_6h_2.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/A549_JQ1_6h_2.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/A549_dBet6_1h_1/A549_dBet6_1h_1.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/A549_dBet6_1h_1.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/A549_dBet6_1h_2/A549_dBet6_1h_2.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/A549_dBet6_1h_2.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/A549_dBet6_6h_1/A549_dBet6_6h_1.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/A549_dBet6_6h_1.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/A549_dBet6_6h_2/A549_dBet6_6h_2.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/A549_dBet6_6h_2.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/HAP1_DMSO_1h_1/HAP1_DMSO_1h_1.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/HAP1_DMSO_1h_1.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/HAP1_DMSO_1h_2/HAP1_DMSO_1h_2.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/HAP1_DMSO_1h_2.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/HAP1_DMSO_6h_1/HAP1_DMSO_6h_1.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/HAP1_DMSO_6h_1.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/HAP1_DMSO_6h_2/HAP1_DMSO_6h_2.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/HAP1_DMSO_6h_2.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/HAP1_JQ1_1h_1/HAP1_JQ1_1h_1.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/HAP1_JQ1_1h_1.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/HAP1_JQ1_1h_2/HAP1_JQ1_1h_2.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/HAP1_JQ1_1h_2.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/HAP1_JQ1_6h_1/HAP1_JQ1_6h_1.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/HAP1_JQ1_6h_1.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/HAP1_JQ1_6h_2/HAP1_JQ1_6h_2.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/HAP1_JQ1_6h_2.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/HAP1_dBet6_1h_1/HAP1_dBet6_1h_1.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/HAP1_dBet6_1h_1.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/HAP1_dBet6_1h_2/HAP1_dBet6_1h_2.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/HAP1_dBet6_1h_2.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/HAP1_dBet6_6h_1/HAP1_dBet6_6h_1.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/HAP1_dBet6_6h_1.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/HAP1_dBet6_6h_2/HAP1_dBet6_6h_2.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/HAP1_dBet6_6h_2.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/K562_DMSO_1h_1/K562_DMSO_1h_1.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/K562_DMSO_1h_1.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/K562_DMSO_1h_2/K562_DMSO_1h_2.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/K562_DMSO_1h_2.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/K562_DMSO_6h_1/K562_DMSO_6h_1.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/K562_DMSO_6h_1.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/K562_DMSO_6h_2/K562_DMSO_6h_2.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/K562_DMSO_6h_2.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/K562_JQ1_1h_1/K562_JQ1_1h_1.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/K562_JQ1_1h_1.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/K562_JQ1_1h_2/K562_JQ1_1h_2.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/K562_JQ1_1h_2.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/K562_JQ1_6h_1/K562_JQ1_6h_1.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/K562_JQ1_6h_1.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/K562_JQ1_6h_2/K562_JQ1_6h_2.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/K562_JQ1_6h_2.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/K562_dBet6_1h_2/K562_dBet6_1h_2.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/K562_dBet6_1h_2.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/K562_dBet6_6h_1/K562_dBet6_6h_1.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/K562_dBet6_6h_1.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/K562_dBet6_6h_2/K562_dBet6_6h_2.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/K562_dBet6_6h_2.small_R1.fastq.gz')
+_download_file(URLH, 'rnaseq_samples/outlier_HAP1_dBet6_1h_1/outlier_HAP1_dBet6_1h_1.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/outlier_HAP1_dBet6_1h_1.small_R1.fastq.gz')
 
-_download_file('rnaseq_samples/sample1/sample1.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/rnaseq_sample1.fq.gz')
-_download_file('rnaseq_samples/sample2/sample2.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/rnaseq_sample2.fq.gz')
-_download_file('rnaseq_samples/sample3/sample3.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/rnaseq_sample3.fq.gz')
-_download_file('rnaseq_samples/sample4/sample4.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/rnaseq_sample4.fq.gz')
+_download_file(URLH, 'chipseq_samples/BRD4_DMSO_1/BRD4_DMSO_1.small_R1.fastq.gz', 'workflows/chipseq/data/example_data/BRD4_DMSO_1.small_R1.fastq.gz')
+_download_file(URLH, 'chipseq_samples/BRD4_DMSO_2/BRD4_DMSO_2.small_R1.fastq.gz', 'workflows/chipseq/data/example_data/BRD4_DMSO_2.small_R1.fastq.gz')
+_download_file(URLH, 'chipseq_samples/BRD4_dBET6_1/BRD4_dBET6_1.small_R1.fastq.gz', 'workflows/chipseq/data/example_data/BRD4_dBET6_1.small_R1.fastq.gz')
+_download_file(URLH, 'chipseq_samples/BRD4_dBET6_2/BRD4_dBET6_2.small_R1.fastq.gz', 'workflows/chipseq/data/example_data/BRD4_dBET6_2.small_R1.fastq.gz')
+_download_file(URLH, 'chipseq_samples/MTHFD1_DMSO_1/MTHFD1_DMSO_1.small_R1.fastq.gz', 'workflows/chipseq/data/example_data/MTHFD1_DMSO_1.small_R1.fastq.gz')
+_download_file(URLH, 'chipseq_samples/MTHFD1_DMSO_2/MTHFD1_DMSO_2.small_R1.fastq.gz', 'workflows/chipseq/data/example_data/MTHFD1_DMSO_2.small_R1.fastq.gz')
+_download_file(URLH, 'chipseq_samples/MTHFD1_dBET6_1/MTHFD1_dBET6_1.small_R1.fastq.gz', 'workflows/chipseq/data/example_data/MTHFD1_dBET6_1.small_R1.fastq.gz')
+_download_file(URLH, 'chipseq_samples/MTHFD1_dBET6_2/MTHFD1_dBET6_2.small_R1.fastq.gz', 'workflows/chipseq/data/example_data/MTHFD1_dBET6_2.small_R1.fastq.gz')
+_download_file(URLH, 'chipseq_samples/input_DMSO_1/input_DMSO_1.small_R1.fastq.gz', 'workflows/chipseq/data/example_data/input_DMSO_1.small_R1.fastq.gz')
+_download_file(URLH, 'chipseq_samples/input_DMSO_2/input_DMSO_2.small_R1.fastq.gz', 'workflows/chipseq/data/example_data/input_DMSO_2.small_R1.fastq.gz')
+_download_file(URLH, 'chipseq_samples/input_dBET6_1/input_dBET6_1.small_R1.fastq.gz', 'workflows/chipseq/data/example_data/input_dBET6_1.small_R1.fastq.gz')
+_download_file(URLH, 'chipseq_samples/input_dBET6_2/input_dBET6_2.small_R1.fastq.gz', 'workflows/chipseq/data/example_data/input_dBET6_2.small_R1.fastq.gz')
+_download_file(URLH, 'chipseq_samples/mockIgG_DMSO_1/mockIgG_DMSO_1.small_R1.fastq.gz', 'workflows/chipseq/data/example_data/mockIgG_DMSO_1.small_R1.fastq.gz')
+_download_file(URLH, 'chipseq_samples/mockIgG_DMSO_2/mockIgG_DMSO_2.small_R1.fastq.gz', 'workflows/chipseq/data/example_data/mockIgG_DMSO_2.small_R1.fastq.gz')
+_download_file(URLH, 'chipseq_samples/mockIgG_dBET6_1/mockIgG_dBET6_1.small_R1.fastq.gz', 'workflows/chipseq/data/example_data/mockIgG_dBET6_1.small_R1.fastq.gz')
+_download_file(URLH, 'chipseq_samples/mockIgG_dBET6_2/mockIgG_dBET6_2.small_R1.fastq.gz', 'workflows/chipseq/data/example_data/mockIgG_dBET6_2.small_R1.fastq.gz')
 
-_download_file('rnaseq_samples/sample1/sample1.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/rnaseq_sample1PE_1.fq.gz')
-_download_file('rnaseq_samples/sample1/sample1.small_R2.fastq.gz', 'workflows/rnaseq/data/example_data/rnaseq_sample1PE_2.fq.gz')
-_download_file('rnaseq_samples/sample2/sample2.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/rnaseq_sample2PE_1.fq.gz')
-_download_file('rnaseq_samples/sample2/sample2.small_R2.fastq.gz', 'workflows/rnaseq/data/example_data/rnaseq_sample2PE_2.fq.gz')
 
-_download_file('chipseq_samples/input_1/input_1.tiny_R1.fastq.gz', 'workflows/chipseq/data/example_data/chipseq_input1.fq.gz')
-_download_file('chipseq_samples/ip_1/ip_1.tiny_R1.fastq.gz', 'workflows/chipseq/data/example_data/chipseq_ip1.fq.gz')
-_download_file('chipseq_samples/input_2/input_2.tiny_R1.fastq.gz', 'workflows/chipseq/data/example_data/chipseq_input2.fq.gz')
-_download_file('chipseq_samples/ip_2/ip_2.tiny_R1.fastq.gz', 'workflows/chipseq/data/example_data/chipseq_ip2.fq.gz')
-_download_file('chipseq_samples/ip_3/ip_3.tiny_R1.fastq.gz', 'workflows/chipseq/data/example_data/chipseq_ip3.fq.gz')
-_download_file('chipseq_samples/ip_4/ip_4.tiny_R1.fastq.gz', 'workflows/chipseq/data/example_data/chipseq_ip4.fq.gz')
-_download_file('chipseq_samples/input_3/input_3.tiny_R1.fastq.gz', 'workflows/chipseq/data/example_data/chipseq_input3.fq.gz')
+
+_download_file(URL, 'rnaseq_samples/sample1/sample1.small_R1.fastq.gz', 'workflows/rnaseq/data/example_data/rnaseq_sample1PE_1.fq.gz')
+_download_file(URL, 'rnaseq_samples/sample1/sample1.small_R2.fastq.gz', 'workflows/rnaseq/data/example_data/rnaseq_sample1PE_2.fq.gz')

include/reference_configs/Test_Homo_sapiens.yaml

@@ -0,0 +1,45 @@
+references:
+  human:
+    small-gencode-v28:
+      metadata:
+        reference_genome_build: 'hg38.p12'
+        reference_effective_genome_count: 2.7e9
+        reference_effective_genome_proportion: 0.87
+
+      genome:
+        url: 'https://github.com/lcdb/lcdb-test-data-human/raw/master/seq/hg38.small.fa'
+        postprocess:
+          function: 'lib.postprocess.utils.convert_fasta_chroms'
+          args: 'https://raw.githubusercontent.com/NICHD-BSPC/chrom-name-mappings/d73fdd4d62ca7e845f9357ea5f08d7a918c17e97/mappings/human/gencode_GRCh38.28_to_ucsc_hg38/mappings_gencode_GRCh38.28_to_ucsc_hg38.tsv'
+
+        indexes:
+          - 'hisat2'
+          - 'bowtie2'
+          - 'star'
+
+      annotation:
+        url: 'https://github.com/lcdb/lcdb-test-data-human/raw/master/annotation/hg38.small.gtf'
+        postprocess:
+          function: 'lib.postprocess.utils.convert_gtf_chroms'
+          args: 'https://raw.githubusercontent.com/NICHD-BSPC/chrom-name-mappings/d73fdd4d62ca7e845f9357ea5f08d7a918c17e97/mappings/human/gencode_GRCh38.28_to_ucsc_hg38/mappings_gencode_GRCh38.28_to_ucsc_hg38.tsv'
+        conversions:
+          - 'refflat'
+          - 'bed12'
+
+      transcriptome:
+        indexes:
+          - 'salmon'
+
+
+    rRNA:
+      genome:
+        url:
+          - 'https://www.arb-silva.de/fileadmin/silva_databases/release_128/Exports/SILVA_128_LSURef_tax_silva_trunc.fasta.gz'
+          - 'https://www.arb-silva.de/fileadmin/silva_databases/release_128/Exports/SILVA_128_SSURef_Nr99_tax_silva_trunc.fasta.gz'
+        postprocess:
+          function: 'lib.common.filter_fastas'
+          args: 'Homo sapiens'
+        indexes:
+          - 'hisat2'
+          - 'bowtie2'
+

requirements-r.txt

@@ -1,9 +1,11 @@
 bioconductor-annotationhub
 bioconductor-apeglm
 bioconductor-biocparallel
+bioconductor-chipseeker
 bioconductor-clusterprofiler
 bioconductor-degreport
 bioconductor-deseq2
+bioconductor-diffbind
 bioconductor-dupradar
 bioconductor-genomeinfodbdata
 bioconductor-genomicfeatures
@@ -27,3 +29,4 @@ r-rmarkdown
 r-sparsem
 r-spp
 r-upsetr
+r-ggupset

test/test_configs/chipseq_one_run.tsv

@@ -1,4 +1,4 @@
 # Samplenames with the same "label" will be considered technical replicates
 samplename	antibody	biological_material	replicate	label	orig_filename
-input_1	input	wingdisc-1	1	input-wingdisc-1	data/example_data/chipseq_input1.fq.gz
-ip_1	gaf	wingdisc-1	1	gaf-wingdisc-1	data/example_data/chipseq_ip1.fq.gz
+BRD4_dBET6_1	dBET6	HAP1_B1	1	BRD4_dBET6_1	data/example_data/BRD4_dBET6_1.small_R1.fastq.gz
+mockIgG_dBET6_1	input	HAP1_B1	1	mockIgG_dBET6_1	data/example_data/mockIgG_dBET6_1.small_R1.fastq.gz

test/test_configs/override_PE.yaml

@@ -0,0 +1,58 @@
+# Due to the way Snakemake recursively merges config items, we need to
+# recursively reset this dictonary to override the default one in order to
+# allow arbitrary other sample names.
+#
+# Use it like this
+#
+#   snakemake --configfile ../../test/override.yaml --config sampletable=/path/to/tsv
+
+
+merged_bigwigs:
+  control_pos:
+    pos: []
+  treatment_all:
+    pos: []
+    neg: []
+
+
+patterns: 'config/rnaseq_patterns.yaml'
+
+# Which key in the `references` dict below to use
+organism: 'dmel'
+
+# If not specified here, use the environment variable REFERENCES_DIR.
+references_dir: 'references_data'
+
+aligner:
+  index: 'hisat2'
+  tag: 'test'
+
+rrna:
+  index: 'bowtie2'
+  tag: 'rRNA'
+
+gtf:
+  tag: "test"
+
+salmon:
+  tag: "test"
+
+fastq_screen:
+  - label: rRNA
+    organism: dmel
+    tag: test
+  - label: PhiX
+    organism: phix
+    tag: default
+  - label: Fly
+    organism: dmel
+    tag: test
+
+
+# See the reference config files in the top level of the repo,
+# include/reference_configs, for inspiration for more species.
+
+include_references:
+  - '../../include/reference_configs/test.yaml'
+  - '../../include/reference_configs/PhiX.yaml'
+  - '../../include/reference_configs/Drosophila_melanogaster.yaml'

test/test_configs/star_override_1pass.yaml

@@ -1,6 +1,6 @@
 aligner:
   index: star
-  tag: test
+  tag: small-gencode-v28
 
 merged_bigwigs:
   control_pos:

test/test_configs/star_override_2pass.yaml

@@ -1,6 +1,6 @@
 aligner:
   index: 'star-twopass'
-  tag: test
+  tag: small-gencode-v28
 
 merged_bigwigs:
   control_pos:

test/test_configs/test_chipseq_regression.yaml

@@ -1,40 +1,38 @@
 #sampletable: 'config/sampletable.tsv'
-organism: 'dmel'
+organism: 'human'
 references_dir: 'references_data'
 peaks_dir: 'data/chipseq_peaks'
 
 chipseq:
   peak_calling:
 
-    - label: gaf-wingdisc-1
+    - label: BRD4_dBET6_1
       algorithm: macs2
       ip:
-        - gaf-wingdisc-1
+        - BRD4_dBET6_1
       control:
-        - input-wingdisc-1
-      effective_genome_count: 7e7
-      extra: '--nomodel --extsize 147'
+        - mockIgG_dBET6_1
+      extra: '--nomodel -p 0.05 --cutoff-analysis'
 
 
 fastq_screen:
   - label: rRNA
-    organism: dmel
-    tag: test
+    organism: human
+    tag: small-gencode-v28
   - label: PhiX
     organism: phix
     tag: default
-  - label: Fly
-    organism: dmel
-    tag: test
+  - label: Human
+    organism: human
+    tag: small-gencode-v28
 
 aligner:
   index: 'bowtie2'
-  tag: 'test'
+  tag: 'small-gencode-v28'
 
 
 merged_bigwigs: {}
 
 include_references:
-  - '../../include/reference_configs/test.yaml'
   - '../../include/reference_configs/PhiX.yaml'
-  - '../../include/reference_configs/Drosophila_melanogaster.yaml'
+  - '../../include/reference_configs/Test_Homo_sapiens.yaml'

test/test_configs/two_samples.tsv

@@ -1,3 +1,3 @@
 samplename	group	layout	orig_filename
-sample1	control	SE	data/example_data/rnaseq_sample1PE_1.fq.gz
-sample2	control	SE	data/example_data/rnaseq_sample2.fq.gz
+A549_dBet6_1h_1	dBet6_1h	SE	data/example_data/A549_dBet6_1h_1.small_R1.fastq.gz
+A549_dBet6_1h_2	dBet6_1h	SE	data/example_data/A549_dBet6_1h_2.small_R1.fastq.gz