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Merge pull request #1003 from maxplanck-ie/allelic_frombam
Allelic frombam
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,49 +1,74 @@ | ||
| import os | ||
|
|
||
| rule link_bam: | ||
| input: | ||
| indir + "/{sample}" + bamExt | ||
| output: | ||
| aligner + "/{sample}.unsorted.bam" if pipeline=="noncoding-rna-seq" else aligner + "/{sample}.bam" | ||
| params: | ||
| input_bai = indir + "/{sample}" + bamExt + ".bai", | ||
| output_bai = aligner + "/{sample}.unsorted.bam.bai" if pipeline=="noncoding-rna-seq" else aligner + "/{sample}.bam.bai" | ||
| run: | ||
| if os.path.exists(params.input_bai) and not os.path.exists(os.path.join(outdir,params.output_bai)): | ||
| os.symlink(params.input_bai,os.path.join(outdir,params.output_bai)) | ||
| if not os.path.exists(os.path.join(outdir,output[0])): | ||
| os.symlink(os.path.join(outdir,input[0]),os.path.join(outdir,output[0])) | ||
|
|
||
| if not pipeline=="noncoding-rna-seq": | ||
| if pipeline=="rna-seq" and "allelic-counting" in mode: | ||
| rule link_bam: | ||
| input: | ||
| indir + "/{sample}.{suffix}" + bamExt | ||
| output: | ||
| "allelic_bams/{sample}.{suffix}" + bamExt | ||
| params: | ||
| input_bai = indir + "/{sample}.{suffix}" + bamExt + ".bai", | ||
| output_bai = "allelic_bams/{sample}.{suffix}" + bamExt + ".bai" | ||
| run: | ||
| if os.path.exists(params.input_bai) and not os.path.exists(os.path.join(outdir,params.output_bai)): | ||
| os.symlink(params.input_bai,os.path.join(outdir,params.output_bai)) | ||
| if not os.path.exists(os.path.join(outdir,output[0])): | ||
| os.symlink(os.path.join(outdir,input[0]),os.path.join(outdir,output[0])) | ||
|
|
||
| rule samtools_index_external: | ||
| input: | ||
| aligner + "/{sample}.bam" | ||
| "allelic_bams/{sample}.{suffix}" + bamExt | ||
| output: | ||
| aligner + "/{sample}.bam.bai" | ||
| "allelic_bams/{sample}.{suffix}" + bamExt + ".bai" | ||
| conda: CONDA_SHARED_ENV | ||
| shell: "if [[ ! -f {output[0]} ]]; then samtools index {input[0]}; fi" | ||
|
|
||
| if not pipeline=="WGBS" or pipeline=="WGBS" and skipBamQC: | ||
| rule link_bam_bai_external: | ||
|
|
||
| else: | ||
| rule link_bam: | ||
| input: | ||
| indir + "/{sample}" + bamExt | ||
| output: | ||
| aligner + "/{sample}.unsorted.bam" if pipeline=="noncoding-rna-seq" else aligner + "/{sample}.bam" | ||
| params: | ||
| input_bai = indir + "/{sample}" + bamExt + ".bai", | ||
| output_bai = aligner + "/{sample}.unsorted.bam.bai" if pipeline=="noncoding-rna-seq" else aligner + "/{sample}.bam.bai" | ||
| run: | ||
| if os.path.exists(params.input_bai) and not os.path.exists(os.path.join(outdir,params.output_bai)): | ||
| os.symlink(params.input_bai,os.path.join(outdir,params.output_bai)) | ||
| if not os.path.exists(os.path.join(outdir,output[0])): | ||
| os.symlink(os.path.join(outdir,input[0]),os.path.join(outdir,output[0])) | ||
|
|
||
| if not pipeline=="noncoding-rna-seq": | ||
| rule samtools_index_external: | ||
| input: | ||
| bam = aligner + "/{sample}.bam", | ||
| bai = aligner + "/{sample}.bam.bai" | ||
| aligner + "/{sample}.bam" | ||
| output: | ||
| bam_out = "filtered_bam/{sample}.filtered.bam", | ||
| bai_out = "filtered_bam/{sample}.filtered.bam.bai", | ||
| shell: """ | ||
| ln -s ../{input.bam} {output.bam_out}; | ||
| ln -s ../{input.bai} {output.bai_out} | ||
| """ | ||
|
|
||
|
|
||
| rule sambamba_flagstat: | ||
| input: | ||
| aligner + "/{sample}.bam" | ||
| output: | ||
| "Sambamba/{sample}.markdup.txt" | ||
| log: "Sambamba/logs/{sample}.flagstat.log" | ||
| conda: CONDA_SAMBAMBA_ENV | ||
| shell: """ | ||
| sambamba flagstat -p {input} > {output} 2> {log} | ||
| """ | ||
| aligner + "/{sample}.bam.bai" | ||
| conda: CONDA_SHARED_ENV | ||
| shell: "if [[ ! -f {output[0]} ]]; then samtools index {input[0]}; fi" | ||
|
|
||
| if not pipeline=="WGBS" or pipeline=="WGBS" and skipBamQC: | ||
| rule link_bam_bai_external: | ||
| input: | ||
| bam = aligner + "/{sample}.bam", | ||
| bai = aligner + "/{sample}.bam.bai" | ||
| output: | ||
| bam_out = "filtered_bam/{sample}.filtered.bam", | ||
| bai_out = "filtered_bam/{sample}.filtered.bam.bai", | ||
| shell: """ | ||
| ln -s ../{input.bam} {output.bam_out}; | ||
| ln -s ../{input.bai} {output.bai_out} | ||
| """ | ||
|
|
||
|
|
||
| rule sambamba_flagstat: | ||
| input: | ||
| aligner + "/{sample}.bam" | ||
| output: | ||
| "Sambamba/{sample}.markdup.txt" | ||
| log: "Sambamba/logs/{sample}.flagstat.log" | ||
| conda: CONDA_SAMBAMBA_ENV | ||
| shell: """ | ||
| sambamba flagstat -p {input} > {output} 2> {log} | ||
| """ |
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