diff --git a/bam2bigwig.sh b/bam2bigwig.sh index 39b7a202a349dd1cd906a268c03405d4a5b0ef96..d71be2ce3116ed820d8ff225d8614029659ec543 100755 --- a/bam2bigwig.sh +++ b/bam2bigwig.sh @@ -126,16 +126,17 @@ samtools view -H ${bam} \ compute_coverage() { - cmd="niceload --noswap -q bedtools genomecov -bg -split ${orient_filter} ${scaling} -ibam ${bam}" + cmd="niceload --noswap bedtools genomecov -bg -split ${orient_filter} ${scaling} -ibam ${bam}" eval ${cmd} \ | mawk '{ print $1"\t"$2"\t"$3"\tid-"NR"\t"$4; }' | sort-bed - \ || error_exit "compute_coverage failed" #|| cleanup && error_exit "compute_coverage failed" } +# TODO: find how to run this with niceload (there may be an issue with the quoting) make_bins() { - cmd="niceload --noswap -q bedmap --faster --echo --mean --delim \"\t\" --skip-unmapped ${bin_file} -" + cmd="bedmap --faster --echo --mean --delim \"\t\" --skip-unmapped ${bin_file} -" eval ${cmd} || error_exit "make_bins failed" #eval ${cmd} || cleanup && error_exit "make_bins failed" } @@ -145,7 +146,7 @@ compute_coverage | make_bins \ #> ${bedgraph} || cleanup && error_exit "generating bedgraph failed" echo "making bigwig" -niceload --noswap -q bedGraphToBigWig ${bedgraph} ${genome_file} ${bigwig} || error_exit "bedGraphToBigWig failed" +niceload --noswap bedGraphToBigWig ${bedgraph} ${genome_file} ${bigwig} || error_exit "bedGraphToBigWig failed" #bedGraphToBigWig ${bedgraph} ${genome_file} ${bigwig} || cleanup && error_exit "bedGraphToBigWig failed" echo "removing ${bedgraph}" diff --git a/small_RNA-seq/small_RNA-seq.snakefile b/small_RNA-seq/small_RNA-seq.snakefile index a01e4d724f31fbe36b46ae403375def85f3dd5e9..1708687a37ebf76a3521787c86f2fc4beae5b78a 100644 --- a/small_RNA-seq/small_RNA-seq.snakefile +++ b/small_RNA-seq/small_RNA-seq.snakefile @@ -1159,7 +1159,7 @@ rule feature_count_reads: shell: """ tmpdir=$(TMPDIR=/var/tmp mktemp --tmpdir -d "feature_{wildcards.lib}_{wildcards.rep}_{wildcards.read_type}_{wildcards.mapping_type}_{wildcards.biotype}_{wildcards.orientation}_{wildcards.feature_type}.XXXXXXXXXX") - cmd="niceload --noswap -q featureCounts {params.min_mapq} -a {params.annot} -o {output.counts} -t {wildcards.feature_type} -g "gene_id" -O -s {params.stranded} --fracOverlap 1 --tmpDir ${{tmpdir}} {input}" + cmd="niceload --noswap featureCounts {params.min_mapq} -a {params.annot} -o {output.counts} -t {wildcards.feature_type} -g "gene_id" -O -s {params.stranded} --fracOverlap 1 --tmpDir ${{tmpdir}} {input}" featureCounts -v 2> {log.log} echo ${{cmd}} 1>> {log.log} eval ${{cmd}} 1>> {log.log} 2> {log.err} || error_exit "featureCounts failed" @@ -1458,7 +1458,7 @@ rule small_RNA_seq_annotate: mem_mb=19150 shell: """ - niceload --noswap -q small_RNA_seq_annotate.py -p {threads} -b {input.sorted_bam} -g {input.merged_gtf} \\ + niceload --noswap small_RNA_seq_annotate.py -p {threads} -b {input.sorted_bam} -g {input.merged_gtf} \\ -r {params.reads_out_dir} -o {params.counts_out_dir} -l {log.mapped_log} """ @@ -1509,7 +1509,7 @@ rule small_RNA_seq_annotate_U: mem_mb=14700 shell: """ - niceload --noswap -q small_RNA_seq_annotate.py -p {threads} -b {input.sorted_bam} -u -g {input.merged_gtf} \\ + niceload --noswap small_RNA_seq_annotate.py -p {threads} -b {input.sorted_bam} -u -g {input.merged_gtf} \\ -r {params.reads_out_dir} -o {params.counts_out_dir} -l {log.mapped_log} """ @@ -2657,7 +2657,7 @@ your deepTools settings and check your input files. #""" try: shell(""" - cmd="niceload --noswap -q bamCoverage -b {input.bam} --skipNAs {params.orient_filter} \\ + cmd="niceload --noswap bamCoverage -b {input.bam} --skipNAs {params.orient_filter} \\ -of=bigwig -bs 10 -p={threads} \\ -o {output.bigwig} \\ 1>> {log.log} 2>> {log.err}" @@ -2722,7 +2722,7 @@ bam2bigwig.sh: bedGraphToBigWig failed """ try: shell(""" - niceload --noswap -q bam2bigwig.sh {input.bam} {params.genome_binned} \\ + niceload --noswap bam2bigwig.sh {input.bam} {params.genome_binned} \\ {wildcards.lib}_{wildcards.rep} {wildcards.orientation} F \\ %f {output.bigwig_norm} \\ > {log.log} 2> {log.err} \\ @@ -3417,22 +3417,25 @@ rule plot_biotype_mean_meta_profile: shell: """ tmpdir=$(TMPDIR=/var/tmp mktemp --tmpdir -d "plot_meta_profile_meta_scale_{wildcards.meta_scale}_{wildcards.read_type}_by_{wildcards.norm}_{wildcards.orientation}_{wildcards.type_set}_{wildcards.biotype}_{wildcards.min_len}_{wildcards.group_type}_{wildcards.lib_group}.XXXXXXXXXX") - niceload --noswap -q computeMatrix scale-regions -S {input.bws} \\ + echo "tmpdir=\\"${{tmpdir}}\\"" 1> {log.log} + cmd="computeMatrix scale-regions -S {input.bws} \\ -R {input.bed} \\ {params.meta_params} \\ -p {threads} \\ - -out ${{tmpdir}}/meta_profile.gz \\ - 1> {log.log} \\ + -out ${{tmpdir}}/meta_profile.gz" + echo "${{cmd}}" 1>> {log.log} + niceload --noswap ${{cmd}} \\ + 1>> {log.log} \\ 2> {log.err} \\ || error_exit "computeMatrix failed" cmd="plotProfile -m ${{tmpdir}}/meta_profile.gz -out {output} \\ -z {wildcards.read_type}_{wildcards.orientation}_on_{wildcards.biotype} \\ - -y \\'{params.y_label}\\' \\ + -y \\"{params.y_label}\\" \\ --samplesLabel {params.labels} \\ --perGroup \\ --labelRotation 90" - echo ${{cmd}} 1>> {log.log} \\ - niceload --noswap -q eval ${{cmd}} \\ + echo "${{cmd}}" 1>> {log.log} + niceload --noswap ${{cmd}} \\ 1>> {log.log} \\ 2>> {log.err} \\ || error_exit "plotProfile failed" @@ -3467,21 +3470,24 @@ rule plot_gene_list_mean_meta_profile: shell: """ tmpdir=$(TMPDIR=/var/tmp mktemp --tmpdir -d "plot_meta_profile_meta_scale_{wildcards.meta_scale}_{wildcards.read_type}_by_{wildcards.norm}_{wildcards.orientation}_{wildcards.type_set}_{wildcards.id_list}_{wildcards.group_type}_{wildcards.lib_group}.XXXXXXXXXX") - niceload --noswap -q computeMatrix scale-regions -S {input.bws} \\ + echo "tmpdir=\\"${{tmpdir}}\\"" 1> {log.log} + cmd="computeMatrix scale-regions -S {input.bws} \\ -R {input.bed} \\ {params.meta_params} \\ -p 1 \\ - -out ${{tmpdir}}/meta_profile.gz \\ - 1> {log.log} \\ + -out ${{tmpdir}}/meta_profile.gz" + echo "${{cmd}}" 1>> {log.log} + niceload --noswap ${{cmd}} \\ + 1>> {log.log} \\ 2> {log.err} \\ || error_exit "computeMatrix failed" cmd="plotProfile -m ${{tmpdir}}/meta_profile.gz -out {output} \\ -z {wildcards.read_type}_{wildcards.orientation}_on_{wildcards.id_list} \\ - -y \\'{params.y_label}\\' \\ + -y \\"{params.y_label}\\" \\ --samplesLabel {params.labels} \\ --perGroup" - echo ${{cmd}} 1>> {log.log} - niceload --noswap -q eval ${{cmd}} \\ + echo "${{cmd}}" 1>> {log.log} + niceload --noswap ${{cmd}} \\ 1>> {log.log} \\ 2>> {log.err} \\ || error_exit "plotProfile failed" @@ -3578,8 +3584,9 @@ rule plot_pi_targets_profile: # We should compute -bs, -b, and -a from PI_MIN shell(""" tmpdir=$(TMPDIR=/var/tmp mktemp --tmpdir -d "plot_pi_targets_profile_{wildcards.lib}_{wildcards.rep}_{wildcards.read_type}_by_{wildcards.norm}_{wildcards.orientation}_{wildcards.biotype}.XXXXXXXXXX") +echo "tmpdir=\\"${{tmpdir}}\\"" 1> {log.log} # 501 and 21 are multiples of 3 -niceload --noswap -q computeMatrix scale-regions -S {input.bigwig} \\ +niceload --noswap computeMatrix scale-regions -S {input.bigwig} \\ -R {input.bed} \\ -bs 3 \\ -b 1002 \\ @@ -3587,15 +3594,15 @@ niceload --noswap -q computeMatrix scale-regions -S {input.bigwig} \\ -a 1002 \\ -p {threads} \\ -out ${{tmpdir}}/meta_profile.gz \\ - 1> {log.log} \\ + 1>> {log.log} \\ 2> {log.err} \\ || error_exit "computeMatrix failed" cmd="plotProfile -m ${{tmpdir}}/meta_profile.gz -out {output.figure} \\ - -y \\'{params.y_label}\\' \\ - --startLabel \\'\\' \\ - --endLabel \\'\\'" -echo ${{cmd}} 1>> {log.log} -niceload --noswap -q eval ${{cmd}} \\ + -y \\"{params.y_label}\\" \\ + --startLabel \\"\\" \\ + --endLabel \\"\\"" +echo "${{cmd}}" 1>> {log.log} +niceload --noswap ${{cmd}} \\ 1>> {log.log} \\ 2>> {log.err} \\ || error_exit "plotProfile failed"