diff --git a/config/config_main.yaml b/config/config_main.yaml index 1256867..503ebc5 100755 --- a/config/config_main.yaml +++ b/config/config_main.yaml @@ -54,13 +54,13 @@ datadirs: resources: # -- references -- # - genome: "test_data/genome_chr6.fa" + genome: "test_data/genome_chr6.fa.gz" transcriptome: "test_data/chr6_cdna.fa.gz" gtf: "test_data/chr6_105.gtf" # -- vcfs -- # gnomad: "test_data/gnomad_chr6.vcf.gz" gsnps: "test_data/1000G_snsp_chr6.vcf.gz" - dbsnps: "test_data/dbsnpALFA_chr6_filt.vcf.gz" + dbsnps: "test_data/dbsnpALFA_chr6.vcf.gz" REDI: "test_data/REDI_chr6.BED.gz" small_exac: "test_data/exac_chr6.vcf.gz" indel: "test_data/indels_chr6.vcf.gz" diff --git a/test_data/1000G_snsp_chr6.vcf.gz b/test_data/1000G_snsp_chr6.vcf.gz index 04a7717..98b326e 100644 Binary files a/test_data/1000G_snsp_chr6.vcf.gz and b/test_data/1000G_snsp_chr6.vcf.gz differ diff --git a/test_data/1000G_snsp_chr6.vcf.gz.tbi b/test_data/1000G_snsp_chr6.vcf.gz.tbi index f165fcc..44a8ad8 100644 Binary files a/test_data/1000G_snsp_chr6.vcf.gz.tbi and b/test_data/1000G_snsp_chr6.vcf.gz.tbi differ diff --git a/test_data/chr6_cdna.fa.gz b/test_data/chr6_cdna.fa.gz index 94a10a6..e9773c1 100644 Binary files a/test_data/chr6_cdna.fa.gz and b/test_data/chr6_cdna.fa.gz differ diff --git a/test_data/dbsnpALFA_chr6_filt.vcf.gz b/test_data/dbsnpALFA_chr6.vcf.gz similarity index 53% rename from test_data/dbsnpALFA_chr6_filt.vcf.gz rename to test_data/dbsnpALFA_chr6.vcf.gz index e991186..2f879d5 100644 Binary files a/test_data/dbsnpALFA_chr6_filt.vcf.gz and b/test_data/dbsnpALFA_chr6.vcf.gz differ diff --git a/test_data/dbsnpALFA_chr6.vcf.gz.tbi b/test_data/dbsnpALFA_chr6.vcf.gz.tbi new file mode 100644 index 0000000..fd8786b Binary files /dev/null and b/test_data/dbsnpALFA_chr6.vcf.gz.tbi differ diff --git a/test_data/dbsnpALFA_chr6_filt.vcf.gz.tbi b/test_data/dbsnpALFA_chr6_filt.vcf.gz.tbi deleted file mode 100644 index 87231c3..0000000 Binary files a/test_data/dbsnpALFA_chr6_filt.vcf.gz.tbi and /dev/null differ diff --git a/test_data/exac_chr6.vcf.gz b/test_data/exac_chr6.vcf.gz index dd6e2b6..29a5e25 100644 Binary files a/test_data/exac_chr6.vcf.gz and b/test_data/exac_chr6.vcf.gz differ diff --git a/test_data/exac_chr6.vcf.gz.tbi b/test_data/exac_chr6.vcf.gz.tbi index 2a04810..1e7978a 100644 Binary files a/test_data/exac_chr6.vcf.gz.tbi and b/test_data/exac_chr6.vcf.gz.tbi differ diff --git a/test_data/genome_chr6.dict b/test_data/genome_chr6.dict index cf6648b..0a74a6d 100644 --- a/test_data/genome_chr6.dict +++ b/test_data/genome_chr6.dict @@ -1,2 +1,2 @@ -@HD VN:1.0 SO:unsorted -@SQ SN:6 LN:31500000 M5:148749b4e34a789ec672d5af905cc509 UR:file:///g100_work/IscrC_ENEO2/repos/RNA-neoflow/test_data/genome_chr6.fa +@HD VN:1.6 +@SQ SN:6 LN:170805979 M5:6a48dfa97e854e3c6f186c8ff973f7dd UR:file:/Volumes/HD2/home/danilo/ENEO/test_data/genome_chr6.fa.gz diff --git a/test_data/genome_chr6.fa.fai b/test_data/genome_chr6.fa.fai index 39da239..0fe15ae 100644 --- a/test_data/genome_chr6.fa.fai +++ b/test_data/genome_chr6.fa.fai @@ -1 +1 @@ -6 31500000 55 60 61 +6 170805979 56 60 61 diff --git a/test_data/genome_chr6.fa b/test_data/genome_chr6.fa.gz similarity index 56% rename from test_data/genome_chr6.fa rename to test_data/genome_chr6.fa.gz index 97f6537..0fb1496 100644 Binary files a/test_data/genome_chr6.fa and b/test_data/genome_chr6.fa.gz differ diff --git a/test_data/genome_chr6.fa.gz.fai b/test_data/genome_chr6.fa.gz.fai new file mode 100644 index 0000000..0fe15ae --- /dev/null +++ b/test_data/genome_chr6.fa.gz.fai @@ -0,0 +1 @@ +6 170805979 56 60 61 diff --git a/test_data/genome_chr6.fa.gz.gzi b/test_data/genome_chr6.fa.gz.gzi new file mode 100644 index 0000000..396859b Binary files /dev/null and b/test_data/genome_chr6.fa.gz.gzi differ diff --git a/test_data/gnomad_chr6.vcf.gz b/test_data/gnomad_chr6.vcf.gz index 42d8628..72f5b9c 100644 Binary files a/test_data/gnomad_chr6.vcf.gz and b/test_data/gnomad_chr6.vcf.gz differ diff --git a/test_data/gnomad_chr6.vcf.gz.tbi b/test_data/gnomad_chr6.vcf.gz.tbi index 7a158cf..5620f13 100644 Binary files a/test_data/gnomad_chr6.vcf.gz.tbi and b/test_data/gnomad_chr6.vcf.gz.tbi differ diff --git a/test_data/indels_chr6.vcf.gz b/test_data/indels_chr6.vcf.gz index f3bd070..fc4cc0a 100644 Binary files a/test_data/indels_chr6.vcf.gz and b/test_data/indels_chr6.vcf.gz differ diff --git a/test_data/indels_chr6.vcf.gz.tbi b/test_data/indels_chr6.vcf.gz.tbi index 59a2614..4e1b80d 100644 Binary files a/test_data/indels_chr6.vcf.gz.tbi and b/test_data/indels_chr6.vcf.gz.tbi differ diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk index 3783b2a..e23981d 100755 --- a/workflow/rules/common.smk +++ b/workflow/rules/common.smk @@ -25,7 +25,7 @@ logpath.mkdir(parents=True, exist_ok=True) germProb_script = config["resources"]["germline_prob_script"] bam_final_path = config["datadirs"]["BQSR"] ref_fasta = config["resources"]["genome"] -ref_dict = ref_fasta.replace(".fa", ".dict") +ref_dict = ref_fasta.replace(".fa.gz", ".dict") intervals_path = os.path.join( config["OUTPUT_FOLDER"] + config["datadirs"]["utils"], "interval-files" ) diff --git a/workflow/rules/index.smk b/workflow/rules/index.smk index f405ef5..86280f0 100755 --- a/workflow/rules/index.smk +++ b/workflow/rules/index.smk @@ -20,8 +20,11 @@ rule star_index: ncpus=8, time="6:00:00", shell: - """STAR --runMode genomeGenerate --runThreadN {threads} --genomeDir {output} \ - --genomeFastaFiles {input.fasta} --sjdbOverhang 100 --sjdbGTFfile {input.gtf}""" + """ + mkfifo genome + zcat {input.fasta} > genome & + STAR --runMode genomeGenerate --runThreadN {threads} --genomeDir {output} \ + --genomeFastaFiles genome --sjdbOverhang 100 --sjdbGTFfile {input.gtf}""" rule salmon_gentrome: