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boyterboyter
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Add support for Snakemake
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-17
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6 files changed

+154
-17
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‎LANGUAGES.md

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@@ -151,7 +151,7 @@ License (license,licence,copying,copying3,unlicense,unlicence,license-mit,licenc
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Lisp (lisp,lsp)
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LLVM IR (ll)
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LOLCODE (lol,lols)
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Lua (lua)
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Lua (lua,luau)
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Luau (luau)
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Lucius (lucius)
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Luna (luna)
@@ -205,7 +205,7 @@ PRQL (prql)
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PSL Assertion (psl)
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Puppet (pp)
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PureScript (purs)
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Python (py)
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Python (py,pyw,pyi)
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Q# (qs)
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QCL (qcl)
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QML (qml)
@@ -232,6 +232,7 @@ Shell (sh,.tcshrc)
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Sieve (sieve)
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SKILL (il)
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Smarty Template (tpl)
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Snakemake (smk,rules,snakefile)
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SNOBOL (sno)
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Softbridge Basic (sbl)
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Solidity (sol)

‎SCC-OUTPUT-REPORT.html

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<th>453</th>
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<th>7424</th>
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<th>1516</th>
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<th>396673</th>
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<th>398173</th>
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<th>3929</th>
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</tr><tr>
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<td>processor/workers_test.go</td>
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<td>0</td>
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<td>2222</td>
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<td>35</td>
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</tr><tr>
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<td>processor/cocomo_test.go</td>
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<td></td>
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<td>37</td>
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<td>8</td>
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<td>4</td>
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<td>25</td>
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<td>6</td>
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<td>699</td>
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<td>23</td>
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</tr><tr>
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<td>processor/bloom.go</td>
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<td></td>
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<td>2</td>
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<td>1051</td>
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<td>29</td>
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</tr><tr>
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<td>processor/cocomo_test.go</td>
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<td></td>
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<td>37</td>
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<td>8</td>
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<td>4</td>
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<td>25</td>
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<td>6</td>
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<td>699</td>
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<td>23</td>
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</tr><tr>
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<td>processor/helpers.go</td>
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<td></td>
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<td>0</td>
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<td>4</td>
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<td>0</td>
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<td>170185</td>
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<td>171685</td>
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<td>5</td>
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</tr></tbody>
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<tfoot><tr>
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<th>453</th>
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<th>7424</th>
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<th>1516</th>
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<th>396673</th>
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<th>398173</th>
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<th>3929</th>
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</tr>
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<tr>

‎examples/language/snakefile.smk

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# 67 lines 50 code 4 comments 13 blanks
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"""
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A sample Snakefile for testing line counting
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"""
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SAMPLES = ["A", "B"]
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# This is a
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# multiline
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# comment
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rule all:
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input:
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"plots/quals.svg"
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'''Sometimes even some
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comments in single quote
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fences.'''
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rule bwa_map:
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input:
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"data/genome.fa", # Inline comments are also supported
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"data/samples/{sample}.fastq"
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output:
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"mapped_reads/{sample}.bam"
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shell:
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"bwa mem {input} | samtools view -Sb - > {output}"
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rule samtools_sort:
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input:
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"mapped_reads/{sample}.bam"
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output:
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"sorted_reads/{sample}.bam"
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shell:
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"samtools sort -T sorted_reads/{wildcards.sample} "
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"-O bam {input} > {output}"
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rule samtools_index:
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input:
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"sorted_reads/{sample}.bam"
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output:
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"sorted_reads/{sample}.bam.bai"
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shell:
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"samtools index {input}"
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rule bcftools_call:
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input:
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fa="data/genome.fa",
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bam=expand("sorted_reads/{sample}.bam", sample=SAMPLES),
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bai=expand("sorted_reads/{sample}.bam.bai", sample=SAMPLES)
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output:
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"calls/all.vcf"
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shell:
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"bcftools mpileup -f {input.fa} {input.bam} | "
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"bcftools call -mv - > {output}"
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rule plot_quals:
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input:
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"calls/all.vcf"
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output:
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"plots/quals.svg"
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script:
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"scripts/plot-quals.py"

‎languages.json

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@@ -5979,6 +5979,75 @@
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"python3"
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]
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},
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"Snakemake": {
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"complexitychecks": [
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"for ",
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"for(",
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"while ",
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"while(",
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"if ",
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"if(",
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"elif ",
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"elif(",
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"else ",
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"else:",
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"match ",
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"match(",
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"try ",
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"try:",
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"except ",
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"except(",
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"finally ",
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"finally:",
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"with ",
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"with (",
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"and ",
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"and(",
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"or ",
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"or("
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],
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"extensions": [
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"smk",
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"rules"
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],
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"line_comment": [
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"#"
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],
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"multi_line": [],
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"quotes": [
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{
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"end": "\"",
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"start": "\""
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},
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{
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"end": "'",
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"start": "'"
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},
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{
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"docString": true,
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"end": "\"\"\"",
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"start": "\"\"\""
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},
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{
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"docString": true,
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"end": "'''",
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"start": "'''"
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},
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{
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"docString": true,
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"end": "\"\"\"",
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"start": "r\"\"\""
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},
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{
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"docString": true,
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"end": "'''",
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"start": "r'''"
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}
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],
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"filenames": [
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"snakefile"
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]
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},
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"PRQL": {
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"complexitychecks": [
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"case ",

‎processor/constants.go

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‎test-all.sh

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@@ -883,7 +883,7 @@ else
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fi
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# Try out specific languages
886-
for i in 'Bosque ' 'Flow9 ' 'Bitbucket Pipeline ' 'Docker ignore ' 'Q# ' 'Futhark ' 'Alloy ' 'Wren ' 'Monkey C ' 'Alchemist ' 'Luna ' 'ignore ' 'XML Schema ' 'Web Services' 'Go ' 'Java ' 'Boo ' 'License ' 'BASH ' 'C Shell ' 'Korn Shell ' 'Makefile ' 'Shell ' 'Zsh ' 'Rakefile ' 'Gemfile ' 'Dockerfile ' 'Yarn ' 'Sieve ' 'F# ' 'Elm ' 'Terraform ' 'Clojure ' 'C# ' 'LLVM IR ' 'HAML ' 'FXML ' 'DM ' 'Nushell ' 'Racket ' 'DOT ' 'YAML ' 'Teal ' 'FSL ' 'INI ' 'Hare ' 'Templ ' 'Cuda ' 'GraphQL ' 'Bicep ' 'Pkl ' 'TypeSpec ' 'LALRPOP '
886+
for i in 'Bosque ' 'Flow9 ' 'Bitbucket Pipeline ' 'Docker ignore ' 'Q# ' 'Futhark ' 'Alloy ' 'Wren ' 'Monkey C ' 'Alchemist ' 'Luna ' 'ignore ' 'XML Schema ' 'Web Services' 'Go ' 'Java ' 'Boo ' 'License ' 'BASH ' 'C Shell ' 'Korn Shell ' 'Makefile ' 'Shell ' 'Zsh ' 'Rakefile ' 'Gemfile ' 'Dockerfile ' 'Yarn ' 'Sieve ' 'F# ' 'Elm ' 'Terraform ' 'Clojure ' 'C# ' 'LLVM IR ' 'HAML ' 'FXML ' 'DM ' 'Nushell ' 'Racket ' 'DOT ' 'YAML ' 'Teal ' 'FSL ' 'INI ' 'Hare ' 'Templ ' 'Cuda ' 'GraphQL ' 'Bicep ' 'Pkl ' 'TypeSpec ' 'LALRPOP ' 'Snakemake '
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do
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if ./scc "examples/language/" | grep -q "$i "; then
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echo -e "${GREEN}PASSED $i Language Check"

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