diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 514b173..383aca1 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -13,8 +13,8 @@ jobs: conda env create --quiet -n testenv -f environment.yml - name: Download test dataset run: | - wget -nv https://export.uppmax.uu.se/snic2020-6-3/minute-testdata/minute-testdata-0.4.tar.gz - tar xf minute-testdata-0.4.tar.gz + wget -nv https://export.uppmax.uu.se/snic2020-6-3/minute-testdata/minute-testdata-0.5.tar.gz + tar xf minute-testdata-0.5.tar.gz - name: Run pipeline run: | source $CONDA/etc/profile.d/conda.sh diff --git a/Snakefile b/Snakefile index ef149f8..5bb8746 100644 --- a/Snakefile +++ b/Snakefile @@ -242,7 +242,7 @@ rule remove_exclude_regions: bam="restricted/{library}.bam" input: bam="dedup/{library}.bam", - bed=config["blacklist_bed"] + bed=config["exclude_regions"], shell: "bedtools" " intersect" diff --git a/config.yaml b/config.yaml index 5eeea7c..20900d9 100644 --- a/config.yaml +++ b/config.yaml @@ -6,7 +6,7 @@ reference_fasta: "ref/mm9.fasta.gz" # Path to a BED file listing the regions to be excluded -blacklist_bed: "dummy_blacklist.bed" +exclude_regions: "exclude.bed" # Length of the 5' UMI umi_length: 6 diff --git a/minute-testdata/Snakefile b/minute-testdata/Snakefile index 80f8ab9..eba4fc8 100644 --- a/minute-testdata/Snakefile +++ b/minute-testdata/Snakefile @@ -18,12 +18,12 @@ rule all: "inp_R2.fastq.gz", "ref.fa", "ref.chrom.sizes", - "blacklist.bed", + "exclude.bed", -rule blacklist: +rule exclude_regions: output: - bed="blacklist.bed" + bed="exclude.bed" run: with open(output.bed, "w") as f: print("mini", 3_100_000, 3_150_000, sep="\t", file=f) diff --git a/minute-testdata/config.yaml b/minute-testdata/config.yaml index a046003..e198f07 100644 --- a/minute-testdata/config.yaml +++ b/minute-testdata/config.yaml @@ -6,16 +6,22 @@ reference_fasta: "ref.fa.gz" # Path to a BED file listing the regions to be excluded -blacklist_bed: "blacklist.bed" - -# Chromosome lengths file (.chrom.sizes or .genome) -chrom_sizes: "ref.chrom.sizes" - -# Effective genome size -genome_size: 3700000 +exclude_regions: "exclude.bed" # Length of the 5' UMI umi_length: 6 # Fragment length (insert size) fragment_size: 150 + + +# +# Optional settings +# +# These usually don’t need to be changed +# + +# The base name of the Bowtie2 index. This is normally found automatically +# in the same folder as the reference_fasta. +# +# - bowtie_index_name: "ref/mm9"