WDL and shell lint

[bkmartinjr]

A number of the workflows/tasks have lint as reported by miniwdl check. Some of the suggestions are worth implementing (eg, quoting).

miniwdl check reference

For example, I ran it on QC/wdl/workflows/standard_qc_haploid.wdl and it reported:

$ miniwdl check hpp_production_workflows/QC/wdl/workflows/standard_qc_haploid.wdl
standard_qc_haploid.wdl
    workflow standardQualityControlHaploid
        (Ln 17, Col 9) UnusedDeclaration, nothing references Boolean isMaleSample
        call asmgene_t.asmgene
        call quast_t.quast
        call meryl_t.runMeryl as meryl
        call merqury_t.merqury
        call yak_t.runYakAssemblyStats as yak
        call consolidate
    task consolidate
        (Ln 135, Col 11) CommandShellCheck, SC2035 Use ./*glob* or -- *glob* so names with dashes won't become options.
        (Ln 135, Col 30) CommandShellCheck, SC2035 Use ./*glob* or -- *glob* so names with dashes won't become options.
    asmgene_t : asmgene.wdl
        workflow runAsmgene (not called)
            call asmgene
                (Ln 4, Col 2) IncompleteCall, required input(s) omitted in call to asmgene (assemblyFasta, genesFasta)
        task asmgene
            (Ln 46, Col 82) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
            (Ln 49, Col 46) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
            (Ln 49, Col 60) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
    merqury_t : merqury.wdl
        workflow runMerqury (not called)
            call merqury
                (Ln 4, Col 5) IncompleteCall, required input(s) omitted in call to merqury (assemblyFasta, kmerTarball)
        task merqury
            (Ln 31, Col 8) CommandShellCheck, SC2034 OMP_NUM_THREADS appears unused. Verify use (or export if used externally).
            (Ln 46, Col 15) CommandShellCheck, SC2207 Prefer mapfile or read -a to split command output (or quote to avoid splitting).
            (Ln 48, Col 19) CommandShellCheck, SC2207 Prefer mapfile or read -a to split command output (or quote to avoid splitting).
            (Ln 49, Col 19) CommandShellCheck, SC2207 Prefer mapfile or read -a to split command output (or quote to avoid splitting).
            (Ln 56, Col 19) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
            (Ln 57, Col 15) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
            (Ln 68, Col 23) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
            (Ln 69, Col 19) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
            (Ln 77, Col 15) CommandShellCheck, SC2206 Quote to prevent word splitting/globbing, or split robustly with mapfile or read -a.
            (Ln 80, Col 8) CommandShellCheck, SC2068 Double quote array expansions to avoid re-splitting elements.
            (Ln 83, Col 17) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
            (Ln 83, Col 40) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
    meryl_t : meryl.wdl
        (Ln 4, Col 1) UnusedImport, no use of workflow, tasks, or structs defined in the imported document shardReads_t
        workflow runMeryl
            scatter readFile
                call extractReads_t.extractReads as sampleReadsExtracted
            scatter readFile
                call extractReads_t.extractReads as maternalReadsExtracted
            scatter readFile
                call extractReads_t.extractReads as paternalReadsExtracted
            call arithmetic_t.sum as sampleReadSize
            call arithmetic_t.sum as maternalReadSize
            call arithmetic_t.sum as paternalReadSize
            call arithmetic_t.sum as allReadSize
            call arithmetic_t.max as sampleReadSizeMax
            call arithmetic_t.max as maternalReadSizeMax
            call arithmetic_t.max as paternalReadSizeMax
            scatter readFile
                call merylCount as sampleMerylCount
            scatter readFile
                call merylCount as maternalMerylCount
            scatter readFile
                call merylCount as paternalMerylCount
            call merylUnionSum as sampleMerylUnionSum
            call merylUnionSum as maternalMerylUnionSum
            call merylUnionSum as paternalMerylUnionSum
            call merylHapmer
        task merylCount
            (Ln 198, Col 8) CommandShellCheck, SC2034 OMP_NUM_THREADS appears unused. Verify use (or export if used externally).
            (Ln 201, Col 11) CommandShellCheck, SC2006 Use $(...) notation instead of legacy backticked `...`.
            (Ln 202, Col 92) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
            (Ln 205, Col 16) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
            (Ln 205, Col 30) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
            (Ln 208, Col 15) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
        task merylHapmer
            (Ln 299, Col 8) CommandShellCheck, SC2034 OMP_NUM_THREADS appears unused. Verify use (or export if used externally).
            (Ln 308, Col 13) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
            (Ln 311, Col 36) CommandShellCheck, SC2035 Use ./*glob* or -- *glob* so names with dashes won't become options.
            (Ln 311, Col 42) CommandShellCheck, SC2035 Use ./*glob* or -- *glob* so names with dashes won't become options.
        task merylUnionSum
            (Ln 244, Col 8) CommandShellCheck, SC2034 OMP_NUM_THREADS appears unused. Verify use (or export if used externally).
        arithmetic_t : arithmetic.wdl
            task max
            task sum
        extractReads_t : extract_reads.wdl
            workflow runExtractReads (not called)
                scatter file
                    call extractReads
            task extractReads
                (Ln 58, Col 65) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
                (Ln 64, Col 12) CommandShellCheck, SC2226 This ln has no destination. Check the arguments, or specify '.' explicitly.
                (Ln 65, Col 56) CommandShellCheck, SC2046 Quote this to prevent word splitting.
                (Ln 65, Col 56) CommandShellCheck, SC2006 Use $(...) notation instead of legacy backticked `...`.
                (Ln 65, Col 106) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
                (Ln 67, Col 46) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
                (Ln 73, Col 19) CommandShellCheck, SC2006 Use $(...) notation instead of legacy backticked `...`.
                (Ln 74, Col 21) CommandShellCheck, SC2053 Quote the right-hand side of == in [[ ]] to prevent glob matching.
                (Ln 75, Col 23) CommandShellCheck, SC2006 Use $(...) notation instead of legacy backticked `...`.
                (Ln 77, Col 13) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
        shardReads_t : shard_reads.wdl
            workflow runShardReads (not called)
                call shardReads
                    (Ln 4, Col 5) IncompleteCall, required input(s) omitted in call to shardReads (readFile)
            task shardReads (not called)
                (Ln 46, Col 97) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
                (Ln 48, Col 88) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
                (Ln 52, Col 24) CommandShellCheck, SC2046 Quote this to prevent word splitting.
                (Ln 52, Col 26) CommandShellCheck, SC2012 Use find instead of ls to better handle non-alphanumeric filenames.
    quast_t : quast.wdl
        workflow runQuast (not called)
            call quast
                (Ln 4, Col 2) IncompleteCall, required input(s) omitted in call to quast (assemblyFasta)
        task quast
            (Ln 34, Col 19) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
            (Ln 37, Col 12) CommandShellCheck, SC2226 This ln has no destination. Check the arguments, or specify '.' explicitly.
            (Ln 44, Col 18) CommandShellCheck, SC2206 Quote to prevent word splitting/globbing, or split robustly with mapfile or read -a.
            (Ln 51, Col 23) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
            (Ln 54, Col 16) CommandShellCheck, SC2226 This ln has no destination. Check the arguments, or specify '.' explicitly.
            (Ln 56, Col 22) CommandShellCheck, SC2206 Quote to prevent word splitting/globbing, or split robustly with mapfile or read -a.
            (Ln 60, Col 14) CommandShellCheck, SC2236 Use -n instead of ! -z.
            (Ln 65, Col 15) CommandShellCheck, SC2206 Quote to prevent word splitting/globbing, or split robustly with mapfile or read -a.
            (Ln 71, Col 17) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
            (Ln 71, Col 38) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
    yak_t : yak.wdl
        (Ln 4, Col 1) UnusedImport, no use of workflow, tasks, or structs defined in the imported document shardReads_t
        workflow runYakAssemblyStats
            (Ln 16, Col 9) UnusedDeclaration, nothing references Int kmerSize
            (Ln 17, Col 9) UnusedDeclaration, nothing references Int shardLinesPerFile
            scatter readFile
                call extractReads_t.extractReads as maternalReadsExtracted
            scatter readFile
                call extractReads_t.extractReads as paternalReadsExtracted
            scatter readFile
                call extractReads_t.extractReads as sampleReadsExtracted
            call arithmetic_t.sum as maternalReadSize
            call arithmetic_t.sum as paternalReadSize
            call arithmetic_t.sum as sampleReadSize
            call yakCount as yakCountMat
            call yakCount as yakCountPat
            call yakCount as yakCountSample
            call yakAssemblyStats
        task yakAssemblyStats
            (Ln 187, Col 81) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
            (Ln 188, Col 81) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
            (Ln 191, Col 112) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
            (Ln 192, Col 112) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
            (Ln 196, Col 8) CommandShellCheck, SC2129 Consider using { cmd1; cmd2; } >> file instead of individual redirects.
            (Ln 196, Col 26) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
            (Ln 197, Col 17) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
            (Ln 197, Col 42) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
            (Ln 198, Col 26) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
            (Ln 199, Col 17) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
            (Ln 199, Col 42) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
            (Ln 200, Col 30) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
            (Ln 201, Col 17) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
            (Ln 201, Col 52) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
            (Ln 202, Col 30) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
            (Ln 203, Col 17) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
            (Ln 203, Col 52) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
            (Ln 206, Col 17) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
            (Ln 206, Col 39) CommandShellCheck, SC2035 Use ./*glob* or -- *glob* so names with dashes won't become options.
        task yakCount
        arithmetic_t : arithmetic.wdl
            task sum
            task max (not called)
        extractReads_t : extract_reads.wdl
            workflow runExtractReads (not called)
                scatter file
                    call extractReads
            task extractReads
                (Ln 58, Col 65) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
                (Ln 64, Col 12) CommandShellCheck, SC2226 This ln has no destination. Check the arguments, or specify '.' explicitly.
                (Ln 65, Col 56) CommandShellCheck, SC2046 Quote this to prevent word splitting.
                (Ln 65, Col 56) CommandShellCheck, SC2006 Use $(...) notation instead of legacy backticked `...`.
                (Ln 65, Col 106) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
                (Ln 67, Col 46) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
                (Ln 73, Col 19) CommandShellCheck, SC2006 Use $(...) notation instead of legacy backticked `...`.
                (Ln 74, Col 21) CommandShellCheck, SC2053 Quote the right-hand side of == in [[ ]] to prevent glob matching.
                (Ln 75, Col 23) CommandShellCheck, SC2006 Use $(...) notation instead of legacy backticked `...`.
                (Ln 77, Col 13) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
        shardReads_t : shard_reads.wdl
            workflow runShardReads (not called)
                call shardReads
                    (Ln 4, Col 5) IncompleteCall, required input(s) omitted in call to shardReads (readFile)
            task shardReads (not called)
                (Ln 46, Col 97) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
                (Ln 48, Col 88) CommandShellCheck, SC2086 Double quote to prevent globbing and word splitting.
                (Ln 52, Col 24) CommandShellCheck, SC2046 Quote this to prevent word splitting.
                (Ln 52, Col 26) CommandShellCheck, SC2012 Use find instead of ls to better handle non-alphanumeric filenames.