Merge pull request #736 from maxplanck-ie/develop

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maxplanck-ie · Dec 22, 2020 · bea1f7b · bea1f7b
2 parents c1ca589 + abee658
commit bea1f7b
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diff --git a/.ci_stuff/test_dag.sh b/.ci_stuff/test_dag.sh
@@ -148,11 +148,11 @@ WC=`DNA-mapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions
 if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 719 ]; then exit 1 ; fi
 #allelic
 WC=`DNA-mapping -m allelic-mapping -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1,strain2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1443 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1297 ]; then exit 1 ; fi
 WC=`DNA-mapping -m allelic-mapping -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --SNPfile allelic_input/snpfile.txt --NMaskedIndex allelic_input/Ngenome .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1426 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1280 ]; then exit 1 ; fi
 WC=`DNA-mapping -m allelic-mapping -i PE_input -o output --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1443 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1297 ]; then exit 1 ; fi
 
 # ChIP-seq
 WC=`ChIP-seq -d BAM_input --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml .ci_stuff/ChIP.sample_config.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
@@ -182,52 +182,52 @@ if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 331 ]; then exit 1 ; fi
 
 # mRNA-seq
 WC=`mRNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 826 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 892 ]; then exit 1 ; fi
 WC=`mRNA-seq -i PE_input -o output --rMats --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 842 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 908 ]; then exit 1 ; fi
 WC=`mRNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
 if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 602 ]; then exit 1 ; fi
 WC=`mRNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 882 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 948 ]; then exit 1 ; fi
 WC=`mRNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment-free,deepTools_qc" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 939 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1005 ]; then exit 1 ; fi
 WC=`mRNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --bcExtract --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 850 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 916 ]; then exit 1 ; fi
 WC=`mRNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --bcExtract --UMIDedup --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 900 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 966 ]; then exit 1 ; fi
 WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 741 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 807 ]; then exit 1 ; fi
 WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
 if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 526 ]; then exit 1 ; fi
 WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment,deepTools_qc" --trim .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 797 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 863 ]; then exit 1 ; fi
 WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" -m "alignment-free,deepTools_qc" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 854 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 920 ]; then exit 1 ; fi
 WC=`mRNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --trim --fastqc .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 909 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 975 ]; then exit 1 ; fi
 WC=`mRNA-seq -i BAM_input/filtered_bam -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 593 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 659 ]; then exit 1 ; fi
 #multiple comparison groups
 WC=`mRNA-seq --mode alignment,alignment-free -i PE_input -o output --rMats --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
 if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 867 ]; then exit 1 ; fi
 #allelic
 WC=`mRNA-seq -m allelic-mapping,deepTools_qc -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1,strain2 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1450 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1370 ]; then exit 1 ; fi
 WC=`mRNA-seq -m allelic-mapping,deepTools_qc -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --SNPfile allelic_input/snpfile.txt --NMaskedIndex allelic_input/Ngenome .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1433 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1353 ]; then exit 1 ; fi
 WC=`mRNA-seq -m allelic-mapping,deepTools_qc -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --VCFfile allelic_input/file.vcf.gz --strains strain1 .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1450 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 1370 ]; then exit 1 ; fi
 
 # noncoding-RNA-seq
 WC=`noncoding-RNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 667 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 733 ]; then exit 1 ; fi
 WC=`noncoding-RNA-seq -i SE_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 582 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 648 ]; then exit 1 ; fi
 WC=`noncoding-RNA-seq -i BAM_input -o output --sampleSheet .ci_stuff/test_sampleSheet.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" --fromBAM .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 503 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 569 ]; then exit 1 ; fi
 #multiple comparison groups
 WC=`noncoding-RNA-seq -i PE_input -o output --sampleSheet .ci_stuff/test_sampleSheet_multiComp.tsv --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`
-if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 689 ]; then exit 1 ; fi
+if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 755 ]; then exit 1 ; fi
 
 # scRNA-seq
 #WC=`scRNAseq -i PE_input -o output --mode Gruen --snakemakeOptions " --dryrun --conda-prefix /tmp" .ci_stuff/organism.yaml | tee >(cat 1>&2) | grep -v "Conda environment" | sed '/^\s*$/d' | wc -l`

diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
@@ -1,6 +1,6 @@
 package:
   name: snakepipes
-  version: 2.4.1
+  version: 2.4.2
 
 source:
   path: ../

diff --git a/docs/content/News.rst b/docs/content/News.rst
@@ -1,6 +1,15 @@
 snakePipes News
 ===============
 
+snakePipes 2.4.2
+----------------
+
+* Deeptools coverage RPKM in mRNA-seq and noncoding-RNA-seq worflows now respects blacklist and ingoreForNorm arguments.
+* In mRNA-seq and noncoding-RNA-seq workflow, deeptools qc will now also output DESeq2 size factor-normalized bigwig files.
+* Fixed conda env for WGBS.
+* Fixed control group ordering in split sample sheets in mRNA-seq and other workflows.
+* Removed rule moving bams from allelic mRNA-seq and DNA-mapping workflows.
+
 snakePipes 2.4.1
 ----------------
 

diff --git a/docs/content/advanced_usage.rst b/docs/content/advanced_usage.rst
@@ -167,8 +167,8 @@ Using AWS or other cloud platforms
 
 There is nothing particularly special about performing computations on AWS or other cloud platforms. Below are a few recommendations, using AWS as an example:
 
- 1. Use a small compute node for initial installation. On AWS a ``t2.small`` node is sufficient for general installation since conda will need 1-2GB RAM for dependency resolution during setup.
- 2. If you can need to create custom indices, then you will need a node with at least 80GB RAM and 10 cores.
+ 1. Use a large compute node for initial installation. On AWS a ``t2.large`` node is sufficient for general installation since conda will need a couple of GB RAM for dependency resolution during setup.
+ 2. If you need to create custom indices, then you will need a node with at least 80GB RAM and 10 cores.
  3. Ensure that you install snakePipes on a separate EBS (or equivalent) storage block. We found that a 200GB ``/data`` partition was most convenient. This absolutely must not be the ``/`` partition, as mounting such a persistent image on other instances will result in paths being changed, which result in needing to modify large numbers of files.
  4. It's usually sufficient to use a single large (e.g., ``m5.24xlarge``) compute node, with 100+ cores and a few hundred GB RAM. This allows one to use the ``--local`` option and not have to deal with the hassle of setting up a proper cluster on AWS. Make sure the then set ``-j`` to the number of available cores on the node, so snakePipes can make the most efficient use of the resources (and minimize your bill).
 

diff --git a/docs/content/setting_up.rst b/docs/content/setting_up.rst
@@ -34,7 +34,7 @@ The easiest way to install snakePipes is via our conda channel. The following co
 
 .. code:: bash
 
-    conda create -n snakePipes -c mpi-ie -c conda-forge -c bioconda snakePipes==2.4.1
+    conda create -n snakePipes -c mpi-ie -c conda-forge -c bioconda snakePipes==2.4.2
 
 This way, the software used within snakePipes do not conflict with the software pre-installed on your terminal or in your python environment.
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -34,7 +34,7 @@ Quick start
 
 .. code:: bash
 
-    conda create -n snakePipes -c mpi-ie -c conda-forge -c bioconda snakePipes==2.4.1
+    conda create -n snakePipes -c mpi-ie -c conda-forge -c bioconda snakePipes==2.4.2
 
 * You can update snakePipes to the latest version available on conda with:
 

diff --git a/snakePipes/__init__.py b/snakePipes/__init__.py
@@ -1 +1 @@
-__version__ = '2.4.1'
+__version__ = '2.4.2'
diff --git a/snakePipes/common_functions.py b/snakePipes/common_functions.py
@@ -262,6 +262,7 @@ def splitSampleSheet(sampleSheet, destination_pfx):
     conditionCol = None
     nameCol = None
     comparisonGroupCol = None
+    batchCol = None
     nCols = None
     d = dict()
     for idx, line in enumerate(f):
@@ -270,6 +271,8 @@ def splitSampleSheet(sampleSheet, destination_pfx):
             conditionCol = cols.index("condition")
             nameCol = cols.index("name")
             comparisonGroupCol = cols.index("group")
+            if "batch" in cols:
+                batchCol = cols.index("batch")
             nCols = len(cols)
             continue
         elif idx == 1:
@@ -280,18 +283,40 @@ def splitSampleSheet(sampleSheet, destination_pfx):
                 conditionCol += 1
                 nameCol += 1
                 comparisonGroupCol += 1
+                if batchCol:
+                    batchCol += 1
+            firstCondition = cols[conditionCol]
         if not len(line.strip()) == 0:
             if cols[comparisonGroupCol] not in d:
                 d[cols[comparisonGroupCol]] = []
-            d[cols[comparisonGroupCol]].append([cols[nameCol], cols[conditionCol]])
+            if batchCol:
+                d[cols[comparisonGroupCol]].append([cols[nameCol], cols[batchCol], cols[conditionCol]])
+            else:
+                d[cols[comparisonGroupCol]].append([cols[nameCol], cols[conditionCol]])
 
     f.close()
+
+    if "All" in d.keys():
+        if batchCol:
+            allCondition = d["All"][0][2]
+        else:
+            allCondition = d["All"][0][1]
+        if allCondition == firstCondition:
+            d["All"].reverse()
     for k in d.keys():
         if k != "All" and "All" in d.keys():
-            d[k].extend(d['All'])
+            if allCondition == firstCondition:
+                for x in d["All"]:
+                    d[k].insert(0, x)
+            else:
+                d[k].extend(d['All'])
+
         outfile = os.path.join("splitSampleSheets", '.'.join([os.path.basename(destination_pfx), k, 'tsv']))
         with open(outfile, 'w') as of:
-            of.write('name\tcondition\n')
+            if batchCol:
+                of.write('name\tbatch\tcondition\n')
+            else:
+                of.write('name\tcondition\n')
             for item in d[k]:
                 of.write('\t'.join(item) + '\n')
 

diff --git a/snakePipes/shared/rscripts/WGBS_metileneQC.Rmd b/snakePipes/shared/rscripts/WGBS_metileneQC.Rmd
@@ -44,7 +44,7 @@ gr = GRanges(seqnames=d$CHROM,
 colnames(elementMetadata(gr)) = gsub("mcols.", "", colnames(elementMetadata(gr)))
 
 # Get the genes
-gtf = makeTxDbFromGFF(gtfFile, format="gtf")
+gtf = GenomicFeatures::makeTxDbFromGFF(gtfFile, format="gtf")
 g = genes(gtf)
 
 # Subset g to only contain seqlevels in gr

diff --git a/snakePipes/shared/rules/SNPsplit.snakefile b/snakePipes/shared/rules/SNPsplit.snakefile
@@ -6,7 +6,8 @@ if aligner == "Bowtie2":
             snp = SNPFile,
             bam = "filtered_bam/{sample}.filtered.bam"
         output:
-            expand("allelic_bams/{{sample}}.filtered.{suffix}.bam", suffix = ['allele_flagged', 'genome1', 'genome2', 'unassigned'])
+            targetbam = expand("allelic_bams/{{sample}}.filtered.{suffix}.bam", suffix = ['allele_flagged', 'genome1', 'genome2', 'unassigned']),
+            tempbam = temp("filtered_bam/{sample}.filtered.sortedByName.bam")
         log: "allelic_bams/logs/{sample}.snp_split.log"
         params:
             pairedEnd = '--paired' if pairedEnd else '',
@@ -22,7 +23,8 @@ elif aligner == "STAR":
             snp = SNPFile,
             bam = aligner+"/{sample}.bam"
         output:
-            expand("allelic_bams/{{sample}}.{suffix}.bam", suffix = ['allele_flagged', 'genome1', 'genome2', 'unassigned'])
+            targetbam = expand("allelic_bams/{{sample}}.{suffix}.bam", suffix = ['allele_flagged', 'genome1', 'genome2', 'unassigned']),
+            tempbam = temp(aligner+"/{sample}.sortedByName.bam")
         log: "allelic_bams/logs/{sample}.snp_split.log"
         params:
             pairedEnd = '--paired' if pairedEnd else '',
@@ -33,32 +35,32 @@ elif aligner == "STAR":
             " -o {params.outdir} --snp_file {input.snp} {input.bam} 2> {log}"
 
 # move the allele-specific bams to another folder
-if aligner == "Bowtie2":
-    rule movebams:
-        input:
-            "allelic_bams/{sample}.filtered.{suffix}.bam"
-        params:
-            otherFile = "filtered_bam/{sample}.filtered.sortedByName.bam"
-        output:
-            temp("allelic_bams/{sample}.{suffix}.unsorted.bam")
-        shell:
-            "mv {input} {output} && \
-            if [ -e {params.otherFile} ]; then rm {params.otherFile}; fi"
-else:
-    rule movebams:
-        input:
-            "allelic_bams/{sample}.{suffix}.bam"
-        params:
-            otherFile = aligner+"/{sample}.sortedByName.bam"
-        output:
-            temp("allelic_bams/{sample}.{suffix}.unsorted.bam")
-        shell:
-            "mv {input} {output} && \
-            if [ -e {params.otherFile} ]; then rm {params.otherFile}; fi"
+#if aligner == "Bowtie2":
+#    rule movebams:
+#        input:
+#            "allelic_bams/{sample}.filtered.{suffix}.bam"
+#        params:
+#            otherFile = "filtered_bam/{sample}.filtered.sortedByName.bam"
+#        output:
+#            temp("allelic_bams/{sample}.{suffix}.unsorted.bam")
+#        shell:
+#            "mv {input} {output} && \
+#            if [ -e {params.otherFile} ]; then rm {params.otherFile}; fi"
+#else:
+#    rule movebams:
+#        input:
+#            "allelic_bams/{sample}.{suffix}.bam"
+#        params:
+#            otherFile = aligner+"/{sample}.sortedByName.bam"
+#        output:
+#            temp("allelic_bams/{sample}.{suffix}.unsorted.bam")
+#        shell:
+#            "mv {input} {output} && \
+#            if [ -e {params.otherFile} ]; then rm {params.otherFile}; fi"
 
 # sort them
 rule BAMsort_allelic:
-    input: "allelic_bams/{sample}.{suffix}.unsorted.bam"
+    input: "allelic_bams/{sample}.filtered.{suffix}.bam" if aligner == "Bowtie2" else "allelic_bams/{sample}.{suffix}.bam"
     output:
         "allelic_bams/{sample}.{suffix}.sorted.bam"
     log: "allelic_bams/logs/{sample}.{suffix}.sort.log"