diff --git a/SUBMIT_CONFIG/slurm/config.yaml b/SUBMIT_CONFIG/slurm/config.yaml
index b2545ee6c42e7ca50464b6aece0d3e1b192112e8..bbdbe9a74ed1e9416d3e023315007a8fec6b1958 100644
--- a/SUBMIT_CONFIG/slurm/config.yaml
+++ b/SUBMIT_CONFIG/slurm/config.yaml
@@ -7,9 +7,9 @@ cluster:
--qos={resources.qos}
--cpus-per-task={threads}
--mem={resources.mem_mb}
- --job-name=GEP.{rule}.{wildcards}.%j
- --output=slurm_logs/{rule}/{wildcards}.%j.out
- --error=slurm_logs/{rule}/{wildcards}.%j.err
+ --job-name=GEP.{rule}.%j
+ --output=slurm_logs/{rule}/%j.out
+ --error=slurm_logs/{rule}/%j.err
--time={resources.time}
diff --git a/Snakefile b/Snakefile
index 3502a10834fd8b20a1bc8d3e1154e13b05b09fe9..8338c8bf15568564278ff21d804796b135b217b3 100644
--- a/Snakefile
+++ b/Snakefile
@@ -201,9 +201,8 @@ elif set(['ID', 'ASM_LEVEL', 'PRI_asm', 'ALT_asm', 'merylDB', 'merylDB_kmer', 'g
dictSamples=samples.T.to_dict('list')
ruleAllQCFiles=[]
- ruleAll=expand(os.path.join(config['Results'],"1_evaluation/{asmID}/KEY_RESULTS/{asmID}_aggregatedResults.tsv"), asmID=list(dictSamples.keys())),\
- os.path.join(config['Results'],"1_evaluation/finalResults/TABLE_OF_RESULTS.tsv"), \
- os.path.join(config['Results'],"1_evaluation/finalResults/FULL_REPORT.pdf")
+ ruleAll=expand(os.path.join(config['Results'],"1_evaluation/{asmID}/KEY_RESULTS/{asmID}_aggregatedSTATS.tsv"), asmID=list(dictSamples.keys())),\
+ os.path.join(config['Results'],"1_evaluation/finalResults/FINAL_REPORT.pdf")
### DOWNLOAD BUSCO LINEAGE (IF IT DOESN'T ALREADY EXIST) ####
@@ -258,7 +257,7 @@ elif set(['ID', 'ASM_LEVEL', 'PRI_asm', 'ALT_asm', 'merylDB', 'merylDB_kmer', 'g
raise ValueError("Error - could not identify lineage please check busco site for a correct prefix")
else:
- raise ValueError('Sample Sheet for not recognised. Please make sure you are using the correct sample sheet')
+ raise ValueError('Sample Sheet not recognised. Please make sure you are using the correct sample sheet')
diff --git a/rules/build_illumina.smk b/rules/build_illumina.smk
index 0680f4a9db7a157cf824298b3311df1d764c459c..b5c4d41a5a7a32ad610fcf1e44e21cc248bc0fe4 100644
--- a/rules/build_illumina.smk
+++ b/rules/build_illumina.smk
@@ -251,7 +251,6 @@ rule merylCount_R1_illumina:
os.path.join(workflow.basedir, "envs/MERYL_MERQURY.yaml")
shell:
"""
- export OMP_NUM_THREADS={threads}
(meryl count k={params.kmer} threads={threads} {input.read1} output {output}) &> {log}
"""
@@ -275,7 +274,6 @@ rule merylCount_R2_illumina:
os.path.join(workflow.basedir, "envs/MERYL_MERQURY.yaml")
shell:
"""
- export OMP_NUM_THREADS={threads}
(meryl count k={params.kmer} threads={threads} {input.read2} output {output}) &> {log}
"""
@@ -306,7 +304,6 @@ rule merylUnion_illumina:
os.path.join(workflow.basedir, "envs/MERYL_MERQURY.yaml")
shell:
"""
- export OMP_NUM_THREADS={threads}
(meryl union-sum {input.read1} {input.read2} output {output}) &> {log}
rm -r {params.removeReadDIR_trimmed}
rm -r {params.removeReadDIR_unzipped}
diff --git a/rules/evaluate.smk b/rules/evaluate.smk
index 2867bd0b5a8b9bbc8e920538262399fb2f3adb54..7e81eff8297cc436ab4fc2e5ba50d5add134cb02 100644
--- a/rules/evaluate.smk
+++ b/rules/evaluate.smk
@@ -5,24 +5,22 @@ def merylDB(wildcards):
return samples.loc[(wildcards.asmID), "merylDB"]
-localrules: symlink_UnzippedFastq_R1_HiC, \
- symlink_UnzippedFastq_R2_HiC, \
- symlink_UnzippedFasta_PRI, \
- symlink_UnzippedFasta_ALT, \
- # symlinkMerylDB, \
-# moveBuscoOutputs, \
- copyKeyResults_GenomeScope2Profiles, \
- copyKeyResults, \
- saveConfigurationAndSampleSheet_createComparisonTablesTSV, \
- IndividualKeyResults_createMD, \
- PretextMaps_createMD, \
- ComparisonTables_createMD, \
- ReportWithoutComparisonTables_createMD, \
- ReportWithoutComparisonTables_createPDF, \
- ComparisonTablesColoured_createHTML, \
- ComparisonTables_createPDF, \
- ComparisonTablesGradient_createHTML, \
- COMBINE_ALL_PDFS
+localrules: symlink_UnzippedFastq_R1_HiC, \
+ symlink_UnzippedFastq_R2_HiC, \
+ symlink_UnzippedFasta_PRI, \
+ symlink_UnzippedFasta_ALT, \
+ KeyResults_GenomescopeProfiles, \
+ KeyResults, \
+ Tables_TSV, \
+ IndividualResults_md, \
+ PretextMaps_md, \
+ Table_md, \
+ Reports_md, \
+ Reports_pdf, \
+ ColouredTable_html, \
+ HeatmapTable_html, \
+ BothTables_pdf, \
+ ConcatAll_pdfs
def HiC_R1_gzipped(wildcards):
return yesGzip_HiC_R1.loc[(wildcards.asmID), "HiC_R1"]
@@ -533,7 +531,7 @@ rule assemblyStats:
-rule copyKeyResults_GenomeScope2Profiles:
+rule KeyResults_GenomescopeProfiles:
input:
gscopeSum=os.path.join(config['Results'], "1_evaluation/{asmID}/GENOMESCOPE_PROFILES/{asmID}_k{kmer}_summary.txt"),
gscopeLog=os.path.join(config['Results'], "1_evaluation/{asmID}/GENOMESCOPE_PROFILES/{asmID}_k{kmer}_log_plot.png"),
@@ -554,7 +552,7 @@ rule copyKeyResults_GenomeScope2Profiles:
-rule copyKeyResults:
+rule KeyResults:
input:
gscopeSum=lambda wildcards: expand(os.path.join(config['Results'], "1_evaluation/{asmID}/GENOMESCOPE_PROFILES/{asmID}_k{kmer}_summary.txt"), asmID=wildcards.asmID, kmer=dictSamples[wildcards.asmID][4]),
# gscopeLog=lambda wildcards: expand(os.path.join(config['Results'], "1_evaluation/{asmID}/GENOMESCOPE_PROFILES/{asmID}_k{kmer}_log_plot.png"), asmID=wildcards.asmID, kmer=dictSamples[wildcards.asmID][4]),
@@ -628,7 +626,7 @@ rule copyKeyResults:
rm {params.rowNames} {params.keyValues}
"""
-rule saveConfigurationAndSampleSheet_createComparisonTablesTSV:
+rule Tables_TSV:
input:
allResults=expand(os.path.join(config['Results'],"1_evaluation/{asmID}/KEY_RESULTS/{asmID}_aggregatedSTATS.tsv"), asmID=list(dictSamples.keys())),
sampleSheet= config['samplesTSV'],
@@ -650,7 +648,7 @@ rule saveConfigurationAndSampleSheet_createComparisonTablesTSV:
sed -i 's/,//g' {output.results}
"""
-rule IndividualKeyResults_createMD:
+rule IndividualResults_md:
input:
os.path.join(config['Results'],"1_evaluation/{asmID}/KEY_RESULTS/{asmID}_aggregatedSTATS.tsv"),
lambda wildcards: expand(os.path.join(config['Results'], "1_evaluation/{asmID}/KEY_RESULTS/{asmID}_k{kmer}_log_plot.png"),asmID=wildcards.asmID, kmer=dictSamples[wildcards.asmID][4]),
@@ -673,7 +671,7 @@ rule IndividualKeyResults_createMD:
-rule PretextMaps_createMD:
+rule PretextMaps_md:
input:
PretextMap=os.path.join(config['Results'], "1_evaluation/{asmID}/HiC_MAPS/{asmID}.HiC.COMBINED.FILTERED_FullMap.png")
output:
@@ -686,7 +684,7 @@ rule PretextMaps_createMD:
script:
os.path.join(workflow.basedir, "scripts/report/pretextMapsToMarkdown.py")
-rule ComparisonTables_createMD:
+rule Table_md:
input:
results=os.path.join(config['Results'],"1_evaluation/finalResults/TABLE_OF_RESULTS.tsv")
output:
@@ -697,7 +695,7 @@ rule ComparisonTables_createMD:
script:
os.path.join(workflow.basedir, "scripts/report/addFullTableForReport.py")
-rule ComparisonTablesColoured_createHTML:
+rule ColouredTable_html:
input:
os.path.join(config['Results'],"1_evaluation/finalResults/TABLE_OF_RESULTS_roundedMB.tsv")
params:
@@ -714,7 +712,7 @@ rule ComparisonTablesColoured_createHTML:
script:
os.path.join(workflow.basedir, "scripts/compare_results/fullTable_heatmap_external.R")
-rule ComparisonTablesGradient_createHTML:
+rule HeatmapTable_html:
input:
os.path.join(config['Results'],"1_evaluation/finalResults/TABLE_OF_RESULTS_roundedMB.tsv")
params:
@@ -731,7 +729,7 @@ rule ComparisonTablesGradient_createHTML:
script:
os.path.join(workflow.basedir, "scripts/compare_results/fullTable_heatmap_internalComparison.R")
-rule ComparisonTables_createPDF:
+rule BothTables_pdf:
input:
coloured=os.path.join(config['Results'],"1_evaluation/finalResults/TABLE_OF_RESULTS_COLOURED.html"),
gradient=os.path.join(config['Results'],"1_evaluation/finalResults/TABLE_OF_RESULTS_GRADIENT.html")
@@ -756,7 +754,7 @@ rule ComparisonTables_createPDF:
-o {output.gradient} --pdf-engine=wkhtmltopdf --pdf-engine-opt="-O" --pdf-engine-opt="Landscape" {input.gradient}) &>> {log}
"""
-rule ReportWithoutComparisonTables_createMD:
+rule Reports_md:
input:
indivMD=[expand(os.path.join(config['Results'],"1_evaluation/{asmID}/KEY_RESULTS/{asmID}_k{kmer}_markdownForReport.md"), asmID=key, kmer=value5) for key, [value1, value2, value3, value4, value5, value6, value7, value8, value9, value10, value11, value12, value13, value14, value15, value16] in dictSamples.items()],
landingPage=os.path.join(workflow.basedir, "scripts/report/reportLandingPage.md"),
@@ -775,7 +773,7 @@ rule ReportWithoutComparisonTables_createMD:
# cat {input.landingPageTABLE} {input.endTableMD} >> {output.endTableMD}
-rule ReportWithoutComparisonTables_createPDF:
+rule Reports_pdf:
input:
md_report=os.path.join(config['Results'],"1_evaluation/finalResults/ALL_individual_REPORTS.md"),
# md_comparison_table=os.path.join(config['Results'],"1_evaluation/finalResults/FullTableMarkdown_wPreamble.md")
@@ -797,7 +795,7 @@ rule ReportWithoutComparisonTables_createPDF:
"""
# (pandoc -o {output.pdf_comparison_table} {input.md_comparison_table} --pdf-engine=tectonic) &>> {log}
-rule COMBINE_ALL_PDFS:
+rule ConcatAll_pdfs:
input:
pdf_report=os.path.join(config['Results'],"1_evaluation/finalResults/ALL_individual_REPORTS.pdf"),
coloured=os.path.join(config['Results'],"1_evaluation/finalResults/TABLE_OF_RESULTS_COLOURED.pdf"),
@@ -807,7 +805,7 @@ rule COMBINE_ALL_PDFS:
pdf_report=os.path.join(config['Results'],"1_evaluation/finalResults/FINAL_REPORT.pdf"),
# pdf_comparison_table=os.path.join(config['Results'],"1_evaluation/finalResults/FULL_TABLE_PDF.pdf")
log:
- os.path.join(config['Results'], "1_evaluation/logs/COMBINE_ALL_PDFS.log")
+ os.path.join(config['Results'], "1_evaluation/logs/ConcatAll_pdfs.log")
conda:
os.path.join(workflow.basedir, "envs/AUXILIARY_PYTHON_SCRIPTS.yaml")
# threads: