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Commit e4972452 authored by Blaise Li's avatar Blaise Li
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Trying to fix niceload quoting issues.

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bam2bigwig.sh
+ 4
− 3
View file @ e4972452
...@@ -126,16 +126,17 @@ samtools view -H ${bam} \ ...@@ -126,16 +126,17 @@ samtools view -H ${bam} \
compute_coverage() 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} \ eval ${cmd} \
| mawk '{ print $1"\t"$2"\t"$3"\tid-"NR"\t"$4; }' | sort-bed - \ | mawk '{ print $1"\t"$2"\t"$3"\tid-"NR"\t"$4; }' | sort-bed - \
|| error_exit "compute_coverage failed" || error_exit "compute_coverage failed"
#|| cleanup && 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() 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} || error_exit "make_bins failed"
#eval ${cmd} || cleanup && error_exit "make_bins failed" #eval ${cmd} || cleanup && error_exit "make_bins failed"
} }
...@@ -145,7 +146,7 @@ compute_coverage | make_bins \ ...@@ -145,7 +146,7 @@ compute_coverage | make_bins \
#> ${bedgraph} || cleanup && error_exit "generating bedgraph failed" #> ${bedgraph} || cleanup && error_exit "generating bedgraph failed"
echo "making bigwig" 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" #bedGraphToBigWig ${bedgraph} ${genome_file} ${bigwig} || cleanup && error_exit "bedGraphToBigWig failed"
echo "removing ${bedgraph}" echo "removing ${bedgraph}"
......
small_RNA-seq/small_RNA-seq.snakefile
+ 31
− 24
View file @ e4972452
...@@ -1159,7 +1159,7 @@ rule feature_count_reads: ...@@ -1159,7 +1159,7 @@ rule feature_count_reads:
shell: shell:
""" """
tmpdir=$(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") 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} featureCounts -v 2> {log.log}
echo ${{cmd}} 1>> {log.log} echo ${{cmd}} 1>> {log.log}
eval ${{cmd}} 1>> {log.log} 2> {log.err} || error_exit "featureCounts failed" eval ${{cmd}} 1>> {log.log} 2> {log.err} || error_exit "featureCounts failed"
...@@ -1458,7 +1458,7 @@ rule small_RNA_seq_annotate: ...@@ -1458,7 +1458,7 @@ rule small_RNA_seq_annotate:
mem_mb=19150 mem_mb=19150
shell: 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} -r {params.reads_out_dir} -o {params.counts_out_dir} -l {log.mapped_log}
""" """
...@@ -1509,7 +1509,7 @@ rule small_RNA_seq_annotate_U: ...@@ -1509,7 +1509,7 @@ rule small_RNA_seq_annotate_U:
mem_mb=14700 mem_mb=14700
shell: 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} -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. ...@@ -2657,7 +2657,7 @@ your deepTools settings and check your input files.
#""" #"""
try: try:
shell(""" 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} \\ -of=bigwig -bs 10 -p={threads} \\
-o {output.bigwig} \\ -o {output.bigwig} \\
1>> {log.log} 2>> {log.err}" 1>> {log.log} 2>> {log.err}"
...@@ -2722,7 +2722,7 @@ bam2bigwig.sh: bedGraphToBigWig failed ...@@ -2722,7 +2722,7 @@ bam2bigwig.sh: bedGraphToBigWig failed
""" """
try: try:
shell(""" 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 \\ {wildcards.lib}_{wildcards.rep} {wildcards.orientation} F \\
%f {output.bigwig_norm} \\ %f {output.bigwig_norm} \\
> {log.log} 2> {log.err} \\ > {log.log} 2> {log.err} \\
...@@ -3417,22 +3417,25 @@ rule plot_biotype_mean_meta_profile: ...@@ -3417,22 +3417,25 @@ rule plot_biotype_mean_meta_profile:
shell: 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") 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} \\ -R {input.bed} \\
{params.meta_params} \\ {params.meta_params} \\
-p {threads} \\ -p {threads} \\
-out ${{tmpdir}}/meta_profile.gz \\ -out ${{tmpdir}}/meta_profile.gz"
1> {log.log} \\ echo "${{cmd}}" 1>> {log.log}
niceload --noswap ${{cmd}} \\
1>> {log.log} \\
2> {log.err} \\ 2> {log.err} \\
|| error_exit "computeMatrix failed" || error_exit "computeMatrix failed"
cmd="plotProfile -m ${{tmpdir}}/meta_profile.gz -out {output} \\ cmd="plotProfile -m ${{tmpdir}}/meta_profile.gz -out {output} \\
-z {wildcards.read_type}_{wildcards.orientation}_on_{wildcards.biotype} \\ -z {wildcards.read_type}_{wildcards.orientation}_on_{wildcards.biotype} \\
-y \\'{params.y_label}\\' \\ -y \\"{params.y_label}\\" \\
--samplesLabel {params.labels} \\ --samplesLabel {params.labels} \\
--perGroup \\ --perGroup \\
--labelRotation 90" --labelRotation 90"
echo ${{cmd}} 1>> {log.log} \\ echo "${{cmd}}" 1>> {log.log}
niceload --noswap -q eval ${{cmd}} \\ niceload --noswap ${{cmd}} \\
1>> {log.log} \\ 1>> {log.log} \\
2>> {log.err} \\ 2>> {log.err} \\
|| error_exit "plotProfile failed" || error_exit "plotProfile failed"
...@@ -3467,21 +3470,24 @@ rule plot_gene_list_mean_meta_profile: ...@@ -3467,21 +3470,24 @@ rule plot_gene_list_mean_meta_profile:
shell: shell:
""" """
tmpdir=$(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") 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} \\ -R {input.bed} \\
{params.meta_params} \\ {params.meta_params} \\
-p 1 \\ -p 1 \\
-out ${{tmpdir}}/meta_profile.gz \\ -out ${{tmpdir}}/meta_profile.gz"
1> {log.log} \\ echo "${{cmd}}" 1>> {log.log}
niceload --noswap ${{cmd}} \\
1>> {log.log} \\
2> {log.err} \\ 2> {log.err} \\
|| error_exit "computeMatrix failed" || error_exit "computeMatrix failed"
cmd="plotProfile -m ${{tmpdir}}/meta_profile.gz -out {output} \\ cmd="plotProfile -m ${{tmpdir}}/meta_profile.gz -out {output} \\
-z {wildcards.read_type}_{wildcards.orientation}_on_{wildcards.id_list} \\ -z {wildcards.read_type}_{wildcards.orientation}_on_{wildcards.id_list} \\
-y \\'{params.y_label}\\' \\ -y \\"{params.y_label}\\" \\
--samplesLabel {params.labels} \\ --samplesLabel {params.labels} \\
--perGroup" --perGroup"
echo ${{cmd}} 1>> {log.log} echo "${{cmd}}" 1>> {log.log}
niceload --noswap -q eval ${{cmd}} \\ niceload --noswap ${{cmd}} \\
1>> {log.log} \\ 1>> {log.log} \\
2>> {log.err} \\ 2>> {log.err} \\
|| error_exit "plotProfile failed" || error_exit "plotProfile failed"
...@@ -3578,8 +3584,9 @@ rule plot_pi_targets_profile: ...@@ -3578,8 +3584,9 @@ rule plot_pi_targets_profile:
# We should compute -bs, -b, and -a from PI_MIN # We should compute -bs, -b, and -a from PI_MIN
shell(""" shell("""
tmpdir=$(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") 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 # 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} \\ -R {input.bed} \\
-bs 3 \\ -bs 3 \\
-b 1002 \\ -b 1002 \\
...@@ -3587,15 +3594,15 @@ niceload --noswap -q computeMatrix scale-regions -S {input.bigwig} \\ ...@@ -3587,15 +3594,15 @@ niceload --noswap -q computeMatrix scale-regions -S {input.bigwig} \\
-a 1002 \\ -a 1002 \\
-p {threads} \\ -p {threads} \\
-out ${{tmpdir}}/meta_profile.gz \\ -out ${{tmpdir}}/meta_profile.gz \\
1> {log.log} \\ 1>> {log.log} \\
2> {log.err} \\ 2> {log.err} \\
|| error_exit "computeMatrix failed" || error_exit "computeMatrix failed"
cmd="plotProfile -m ${{tmpdir}}/meta_profile.gz -out {output.figure} \\ cmd="plotProfile -m ${{tmpdir}}/meta_profile.gz -out {output.figure} \\
-y \\'{params.y_label}\\' \\ -y \\"{params.y_label}\\" \\
--startLabel \\'\\' \\ --startLabel \\"\\" \\
--endLabel \\'\\'" --endLabel \\"\\""
echo ${{cmd}} 1>> {log.log} echo "${{cmd}}" 1>> {log.log}
niceload --noswap -q eval ${{cmd}} \\ niceload --noswap ${{cmd}} \\
1>> {log.log} \\ 1>> {log.log} \\
2>> {log.err} \\ 2>> {log.err} \\
|| error_exit "plotProfile failed" || error_exit "plotProfile failed"
......
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