Adding in many staging wrappers

MANIFEST.in

@@ -5,3 +5,8 @@ recursive-include docs *.rst
 recursive-include snakescale/wrappers Snakefile
 recursive-include snakescale/wrappers *.yaml wrapper.py
 recursive-include snakescale/wrappers *.bed *.genome
+recursive-include snakescale/wrappers *.bam *.bai *vcf *vcf.gz
+recursive-include snakescale/wrappers *.fa *.fasta *.fa.gz *.fasta.gz
+recursive-include snakescale/wrappers *mutations.txt  # dwgsim wrapper
+
+

snakescale/wrappers/latest/bwa/mem/environment.yaml

@@ -0,0 +1,5 @@
+channels:
+  - bioconda
+dependencies:
+  - bwa
+  - picard

snakescale/wrappers/latest/bwa/mem/meta.yaml

@@ -0,0 +1,4 @@
+name: bwa mem
+description: Align sequence alignment data.
+authors:
+  - Clint Valentine

snakescale/wrappers/latest/bwa/mem/test/Snakefile

@@ -0,0 +1,26 @@
+from snakescale import scale
+
+rule align_with_bwa_mem:
+    input:
+        reference='data/reference.fa',
+        unmapped_bam='data/infile.bam'
+    output: 'data/result.bam'
+    params:
+        sam_to_fastq={
+            'clipping_action': 'N',
+            'clipping_attribute': 'XT',
+            'clipping_min_length': 25,
+            'interleave': True,
+            'include_non_pf_reads': False
+        },
+        bwa_mem={'p': True, 'v': 2},
+        merge_bam_alignment={
+            'aligner_proper_pair_flags': False,
+            'attributes_to_retain': ['X0', 'ZS', 'ZI', 'ZM', 'ZC', 'ZN'],
+            'clip_adapters': False,
+            'expected_orientations': 'FR',
+            'max_insertions_or_deletions': -1,
+            'sort_order': 'coordinate'
+        }
+    log: 'data/result.log'
+    wrapper: scale('bwa', 'mem')

snakescale/wrappers/latest/bwa/mem/test/data/reference.fa

@@ -0,0 +1,10 @@
+>NC_001416.1 Enterobacteria phage lambda, complete genome
+GGGCGGCGACCTCGCGGGTTTTCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCG
+TCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGACAGGTGCTGAAAGCGAGGC
+TTTTTGGCCTCTGTCGTTTCCTTTCTCTGTTTTTGTCCGTGGAATGAACAATGGAAGTCAACAAAAAGCA
+GCTGGCTGACATTTTCGGTGCGAGTATCCGTACCATTCAGAACTGGCAGGAACAGGGAATGCCCGTTCTG
+CGAGGCGGTGGCAAGGGTAATGAGGTGCTTTATGACTCTGCCGCCGTCATAAAATGGTATGCCGAAAGGG
+ATGCTGAAATTGAGAACGAAAAGCTGCGCCGGGAGGTTGAAGAACTGCGGCAGGCCAGCGAGGCAGATCT
+CCAGCCAGGAACTATTGAGTACGAACGCCATCGACTTACGCGTGCGCAGGCCGACGCACAGGAACTGAAG
+AATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTG
+AAATTGCCAGTATTCTCGACGGGCTCCCCCTGTCGGTGCAGCGGCGTTTTCCGGAACTGGAAAACCGACA

snakescale/wrappers/latest/bwa/mem/wrapper.py

@@ -0,0 +1,44 @@
+"""Snakemake wrapper for bwa mem ClipBam."""
+
+__author__ = 'clintval'
+__copyright__ = 'Copyright 2018, Clint Valentine'
+__email__ = '[email protected]'
+__license__ = 'MIT'
+
+from snakemake.shell import shell
+
+from snakescale.utils import collect_jvm_resources
+from snakescale.utils import collect_picard_style_jvm_resources
+from snakescale.utils import make_bwa_params
+from snakescale.utils import make_picard_params
+
+extra = snakemake.params.get('extra', '')
+extra += collect_jvm_resources()
+extra += collect_picard_style_jvm_resources()
+
+sam_to_fastq_params = make_picard_params(snakemake.params.get('sam_to_fastq', {}))
+bwa_mem_params = make_bwa_params(snakemake.params.get('bwa_mem', {}))
+merge_bam_alignment_params = make_picard_params(snakemake.params.get('merge_bam_alignment', {}))
+
+log = snakemake.log_fmt_shell(stdout=False, stderr=True, append=True)
+
+shell(
+    'picard {extra} SamToFastq'
+    ' INPUT={snakemake.input.unmapped_bam}'
+    ' FASTQ=/dev/stdout'
+    ' {sam_to_fastq_params}'
+    ' {log}'
+    ' | bwa mem'
+    ' -t {snakemake.threads}'
+    ' {snakemake.input.reference}'
+    ' /dev/stdin'
+    ' {bwa_mem_params}'
+    ' {log}'
+    ' | picard {extra} MergeBamAlignment '
+    ' UNMAPPED={snakemake.input.unmapped_bam}'
+    ' REFERENCE_SEQUENCE={snakemake.input.reference}'
+    ' ALIGNED=/dev/stdin'
+    ' OUTPUT={snakemake.output}'
+    ' {merge_bam_alignment_params}'
+    ' {log}'
+)

snakescale/wrappers/latest/dwgsim/environment.yaml

@@ -0,0 +1,4 @@
+channels:
+  - bioconda
+dependencies:
+  - dwgsim

snakescale/wrappers/latest/dwgsim/meta.yaml

@@ -0,0 +1,4 @@
+name: dwgsim
+description: Simulate sequencing reads.
+authors:
+  - Clint Valentine

snakescale/wrappers/latest/dwgsim/test/Snakefile

@@ -0,0 +1,31 @@
+from snakescale import scale
+
+output_prefix = 'data/result'
+
+rule dwgsim:
+    input: 'data/reference.fa'
+    output: 
+        output_prefix + '.bfast.fastq',
+        output_prefix + '.bwa.read1.fastq',
+        output_prefix + '.bwa.read2.fastq',
+        output_prefix + '.mutations.txt',
+        output_prefix + '.mutations.vcf',
+    params:
+        output_prefix=output_prefix,
+        r1=141,      # Length of read one (flag `-1`)
+        r2=141,      # Length of read two (flag `-2`)
+        c=0,         # Generate reads for platform `Illumina`
+        d=150,       # Outer distance between two ends for pairs
+        s=50,        # Standard deviation of the distance between pairs
+        C=100,       # Mean coverage across available positions
+        e=0.003,     # Error rate per base in first read
+        E=0.004,     # Error rate per base in second read
+        r=0.001,     # Mutation rate
+        F=0.0001,    # Somatic mutation rate
+        R=0,         # Fraction of mutations that are indel
+        X=0,         # Probability an indel is extended
+        y=0.01,      # Probability of a random DNA read
+        n=10,        # Maximum number of Ns allowed in a given read
+        z=42,        # Random seed
+    log: 'data/result.log'
+    wrapper: scale('dwgsim')

snakescale/wrappers/latest/dwgsim/test/data/reference.fa

@@ -0,0 +1,10 @@
+>NC_001416.1 Enterobacteria phage lambda, complete genome
+GGGCGGCGACCTCGCGGGTTTTCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCG
+TCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGACAGGTGCTGAAAGCGAGGC
+TTTTTGGCCTCTGTCGTTTCCTTTCTCTGTTTTTGTCCGTGGAATGAACAATGGAAGTCAACAAAAAGCA
+GCTGGCTGACATTTTCGGTGCGAGTATCCGTACCATTCAGAACTGGCAGGAACAGGGAATGCCCGTTCTG
+CGAGGCGGTGGCAAGGGTAATGAGGTGCTTTATGACTCTGCCGCCGTCATAAAATGGTATGCCGAAAGGG
+ATGCTGAAATTGAGAACGAAAAGCTGCGCCGGGAGGTTGAAGAACTGCGGCAGGCCAGCGAGGCAGATCT
+CCAGCCAGGAACTATTGAGTACGAACGCCATCGACTTACGCGTGCGCAGGCCGACGCACAGGAACTGAAG
+AATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTG
+AAATTGCCAGTATTCTCGACGGGCTCCCCCTGTCGGTGCAGCGGCGTTTTCCGGAACTGGAAAACCGACA