ShellCheck spans are sometimes off

[a-frantz]

Copy and pasting the full report from the workflows repo:
sprocket lint --shellcheck --except TrailingComma --except ContainerValue --local-only --no-color .

note[ShellCheck]: Remove quotes from right-hand side of =~ to match as a regex rather than literally.
    ┌─ /Users/afrantz/workflows/data_structures/read_group.wdl:200:43
    │
200 │                 || [[ ~{read_group.ID} =~ ~{restrictive_pattern} ]]
    │ ╭─────────────────────────────────────────────^
    │ │ ╭───────────────────────────────────────────'
201 │ │ │             then
    │ ╰─│^ SC2076[warning]: Remove quotes from right-hand side of =~ to match as a regex rather than literally.
    │   ╰' more info: https://www.shellcheck.net/wiki/SC2076
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Quote this to prevent word splitting.
    ┌─ /Users/afrantz/workflows/data_structures/read_group.wdl:212:14
    │
212 │         if [ $(echo "~{sep(" ", required_fields)}" | grep -Ewc "SM") -eq 1 ]
    │              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    │              │
    │              SC2046[warning]: Quote this to prevent word splitting.
    │              more info: https://www.shellcheck.net/wiki/SC2046
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Remove quotes from right-hand side of =~ to match as a regex rather than literally.
    ┌─ /Users/afrantz/workflows/data_structures/read_group.wdl:225:53
    │
225 │                     || [[ "~{read_group.SM}" =~ ~{restrictive_pattern} ]]
    │ ╭───────────────────────────────────────────────────────^
    │ │ ╭─────────────────────────────────────────────────────'
226 │ │ │                 then
    │ ╰─│────^ SC2076[warning]: Remove quotes from right-hand side of =~ to match as a regex rather than literally.
    │   ╰────' more info: https://www.shellcheck.net/wiki/SC2076
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Quote this to prevent word splitting.
    ┌─ /Users/afrantz/workflows/data_structures/read_group.wdl:238:14
    │
238 │         if [ $(echo "~{sep(" ", required_fields)}" | grep -Ewc "BC") -eq 1 ]
    │              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    │              │
    │              SC2046[warning]: Quote this to prevent word splitting.
    │              more info: https://www.shellcheck.net/wiki/SC2046
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Quote this to prevent word splitting.
    ┌─ /Users/afrantz/workflows/data_structures/read_group.wdl:254:14
    │
254 │         if [ $(echo "~{sep(" ", required_fields)}" | grep -Ewc "CN") -eq 1 ]
    │              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    │              │
    │              SC2046[warning]: Quote this to prevent word splitting.
    │              more info: https://www.shellcheck.net/wiki/SC2046
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Quote this to prevent word splitting.
    ┌─ /Users/afrantz/workflows/data_structures/read_group.wdl:270:14
    │
270 │         if [ $(echo "~{sep(" ", required_fields)}" | grep -Ewc "DS") -eq 1 ]
    │              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    │              │
    │              SC2046[warning]: Quote this to prevent word splitting.
    │              more info: https://www.shellcheck.net/wiki/SC2046
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Quote this to prevent word splitting.
    ┌─ /Users/afrantz/workflows/data_structures/read_group.wdl:286:14
    │
286 │         if [ $(echo "~{sep(" ", required_fields)}" | grep -Ewc "DT") -eq 1 ]
    │              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    │              │
    │              SC2046[warning]: Quote this to prevent word splitting.
    │              more info: https://www.shellcheck.net/wiki/SC2046
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Quote this to prevent word splitting.
    ┌─ /Users/afrantz/workflows/data_structures/read_group.wdl:302:14
    │
302 │         if [ $(echo "~{sep(" ", required_fields)}" | grep -Ewc "FO") -eq 1 ]
    │              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    │              │
    │              SC2046[warning]: Quote this to prevent word splitting.
    │              more info: https://www.shellcheck.net/wiki/SC2046
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Quote this to prevent word splitting.
    ┌─ /Users/afrantz/workflows/data_structures/read_group.wdl:318:14
    │
318 │         if [ $(echo "~{sep(" ", required_fields)}" | grep -Ewc "KS") -eq 1 ]
    │              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    │              │
    │              SC2046[warning]: Quote this to prevent word splitting.
    │              more info: https://www.shellcheck.net/wiki/SC2046
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Quote this to prevent word splitting.
    ┌─ /Users/afrantz/workflows/data_structures/read_group.wdl:334:14
    │
334 │         if [ $(echo "~{sep(" ", required_fields)}" | grep -Ewc "LB") -eq 1 ]
    │              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    │              │
    │              SC2046[warning]: Quote this to prevent word splitting.
    │              more info: https://www.shellcheck.net/wiki/SC2046
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Quote this to prevent word splitting.
    ┌─ /Users/afrantz/workflows/data_structures/read_group.wdl:350:14
    │
350 │         if [ $(echo "~{sep(" ", required_fields)}" | grep -Ewc "PG") -eq 1 ]
    │              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    │              │
    │              SC2046[warning]: Quote this to prevent word splitting.
    │              more info: https://www.shellcheck.net/wiki/SC2046
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Quote this to prevent word splitting.
    ┌─ /Users/afrantz/workflows/data_structures/read_group.wdl:366:14
    │
366 │         if [ $(echo "~{sep(" ", required_fields)}" | grep -Ewc "PI") -eq 1 ]
    │              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    │              │
    │              SC2046[warning]: Quote this to prevent word splitting.
    │              more info: https://www.shellcheck.net/wiki/SC2046
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Quote this to prevent word splitting.
    ┌─ /Users/afrantz/workflows/data_structures/read_group.wdl:382:14
    │
382 │         if [ $(echo "~{sep(" ", required_fields)}" | grep -Ewc "PL") -eq 1 ]
    │              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    │              │
    │              SC2046[warning]: Quote this to prevent word splitting.
    │              more info: https://www.shellcheck.net/wiki/SC2046
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Quote this to prevent word splitting.
    ┌─ /Users/afrantz/workflows/data_structures/read_group.wdl:398:14
    │
398 │         if [ $(echo "~{sep(" ", required_fields)}" | grep -Ewc "PM") -eq 1 ]
    │              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    │              │
    │              SC2046[warning]: Quote this to prevent word splitting.
    │              more info: https://www.shellcheck.net/wiki/SC2046
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Quote this to prevent word splitting.
    ┌─ /Users/afrantz/workflows/data_structures/read_group.wdl:414:14
    │
414 │         if [ $(echo "~{sep(" ", required_fields)}" | grep -Ewc "PU") -eq 1 ]
    │              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    │              │
    │              SC2046[warning]: Quote this to prevent word splitting.
    │              more info: https://www.shellcheck.net/wiki/SC2046
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Double quote to prevent globbing and word splitting.
    ┌─ /Users/afrantz/workflows/tools/arriba.wdl:285:17
    │
285 │                 $fasta_name \
    │ ╭───────────────────^
    │ │ ╭─────────────────'
286 │ │ │             ~{fusions} \
    │ ╰─│─^ SC2086[info]: Double quote to prevent globbing and word splitting.
    │   ╰─' more info: https://www.shellcheck.net/wiki/SC2086
    │
    = fix: did you mean `"$fasta_name"`?

note[ShellCheck]: Double quote to prevent globbing and word splitting.
    ┌─ /Users/afrantz/workflows/tools/arriba.wdl:385:17
    │
385 │                 $gtf_name \
    │ ╭───────────────────^
    │ │ ╭─────────────────'
386 │ │ │             ~{prefix}.annotated.tsv
    │ ╰─│─^ SC2086[info]: Double quote to prevent globbing and word splitting.
    │   ╰─' more info: https://www.shellcheck.net/wiki/SC2086
    │
    = fix: did you mean `"$gtf_name"`?

note[ShellCheck]: Instead of 'let expr', prefer (( expr )) .
   ┌─ /Users/afrantz/workflows/tools/bwa.wdl:62:9
   │
62 │         let "samtools_cores = $n_cores - 1"
   │         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
   │         │
   │         SC2219[style]: Instead of 'let expr', prefer (( expr )) .
   │         more info: https://www.shellcheck.net/wiki/SC2219
   │
   = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Instead of 'let expr', prefer (( expr )) .
    ┌─ /Users/afrantz/workflows/tools/bwa.wdl:161:9
    │
161 │         let "samtools_cores = $n_cores - 1"
    │         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    │         │
    │         SC2219[style]: Instead of 'let expr', prefer (( expr )) .
    │         more info: https://www.shellcheck.net/wiki/SC2219
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: This ln has no destination. Check the arguments, or specify '.' explicitly.
    ┌─ /Users/afrantz/workflows/tools/bwa.wdl:167:9
    │
167 │         ln -s ~{read_one_fastq_gz}
    │         ^^^^^^^^^^^^^^^^^^^^^^^^^^
    │         │
    │         SC2226[warning]: This ln has no destination. Check the arguments, or specify '.' explicitly.
    │         more info: https://www.shellcheck.net/wiki/SC2226
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: This ln has no destination. Check the arguments, or specify '.' explicitly.
    ┌─ /Users/afrantz/workflows/tools/bwa.wdl:168:9
    │
168 │         ln -s ~{read_two_fastq_gz}
    │         ^^^^^^^^^^^^^^^^^^^^^^^^^^
    │         │
    │         SC2226[warning]: This ln has no destination. Check the arguments, or specify '.' explicitly.
    │         more info: https://www.shellcheck.net/wiki/SC2226
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Instead of 'let expr', prefer (( expr )) .
    ┌─ /Users/afrantz/workflows/tools/bwa.wdl:257:9
    │
257 │         let "samtools_cores = $n_cores - 1"
    │         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    │         │
    │         SC2219[style]: Instead of 'let expr', prefer (( expr )) .
    │         more info: https://www.shellcheck.net/wiki/SC2219
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: This ln has no destination. Check the arguments, or specify '.' explicitly.
    ┌─ /Users/afrantz/workflows/tools/bwa.wdl:263:9
    │
263 │         ln -sf ~{read_one_fastq_gz}
    │         ^^^^^^^^^^^^^^^^^^^^^^^^^^^
    │         │
    │         SC2226[warning]: This ln has no destination. Check the arguments, or specify '.' explicitly.
    │         more info: https://www.shellcheck.net/wiki/SC2226
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Prefer escape over ending quote to make $ literal. Instead of "It costs $"5, use "It costs \$5".
   ┌─ /Users/afrantz/workflows/tools/estimate.wdl:39:34
   │
39 │         filtered <- infile[infile$"Gene.name" %in% common_genes[['GeneSymbol']], ]
   │                                  ^
   │                                  │
   │                                  SC1135[style]: Prefer escape over ending quote to make $ literal. Instead of "It costs $"5, use "It costs \$5".
   │                                  more info: https://www.shellcheck.net/wiki/SC1135
   │
   = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Double quote to prevent globbing and word splitting.
    ┌─ /Users/afrantz/workflows/tools/ngsderive.wdl:355:24
    │
355 │         mv "$(basename ~{bam}.junctions.tsv)" "~{prefix}.junctions.tsv"
    │                        ^^^^^^
    │                        │
    │                        SC2086[info]: Double quote to prevent globbing and word splitting.
    │                        more info: https://www.shellcheck.net/wiki/SC2086
    │
    = fix: did you mean `"${WDL}"`?

note[ShellCheck]: Double quote to prevent globbing and word splitting.
    ┌─ /Users/afrantz/workflows/tools/picard.wdl:235:50
    │
235 │             && [ "$(grep -Ec "$GREP_PATTERN" ~{outfile_name})" -gt 0 ]
    │                                                  ^^^^^^^^^^^^^^^
    │                                                  │
    │                                                  SC2086[info]: Double quote to prevent globbing and word splitting.
    │                                                  more info: https://www.shellcheck.net/wiki/SC2086
    │
    = fix: did you mean `"${WDL9CgEvEsk9}"`?

note[ShellCheck]: Couldn't parse this escaped char. Fix to allow more checks.
     ┌─ /Users/afrantz/workflows/tools/picard.wdl:1034:3
     │
1034 │     >>>
     │   ^
     │   │
     │   SC1073[error]: Couldn't parse this escaped char. Fix to allow more checks.
     │   more info: https://www.shellcheck.net/wiki/SC1073
     │
     = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Instead of 'let expr', prefer (( expr )) .
   ┌─ /Users/afrantz/workflows/tools/samtools.wdl:98:9
   │
98 │         let "n_cores -= 1"
   │         ^^^^^^^^^^^^^^^^^
   │         │
   │         SC2219[style]: Instead of 'let expr', prefer (( expr )) .
   │         more info: https://www.shellcheck.net/wiki/SC2219
   │
   = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Instead of 'let expr', prefer (( expr )) .
    ┌─ /Users/afrantz/workflows/tools/samtools.wdl:199:9
    │
199 │         let "n_cores -= 1"
    │         ^^^^^^^^^^^^^^^^^
    │         │
    │         SC2219[style]: Instead of 'let expr', prefer (( expr )) .
    │         more info: https://www.shellcheck.net/wiki/SC2219
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Instead of 'let expr', prefer (( expr )) .
    ┌─ /Users/afrantz/workflows/tools/samtools.wdl:257:9
    │
257 │         let "n_cores -= 1"
    │         ^^^^^^^^^^^^^^^^^
    │         │
    │         SC2219[style]: Instead of 'let expr', prefer (( expr )) .
    │         more info: https://www.shellcheck.net/wiki/SC2219
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Instead of 'let expr', prefer (( expr )) .
    ┌─ /Users/afrantz/workflows/tools/samtools.wdl:322:9
    │
322 │         let "n_cores -= 1"
    │         ^^^^^^^^^^^^^^^^^
    │         │
    │         SC2219[style]: Instead of 'let expr', prefer (( expr )) .
    │         more info: https://www.shellcheck.net/wiki/SC2219
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Double quote to prevent globbing and word splitting.
    ┌─ /Users/afrantz/workflows/tools/samtools.wdl:333:17
    │
333 │                 ~{bam}
    │ ╭───────────────────^
    │ │ ╭─────────────────'
334 │ │ │         )"
    │ ╰─│───^ SC2086[info]: Double quote to prevent globbing and word splitting.
    │   ╰───' more info: https://www.shellcheck.net/wiki/SC2086
    │
    = fix: did you mean `"${WDL}"`?

note[ShellCheck]: Instead of 'let expr', prefer (( expr )) .
    ┌─ /Users/afrantz/workflows/tools/samtools.wdl:465:9
    │
465 │         let "n_cores -= 1"
    │         ^^^^^^^^^^^^^^^^^
    │         │
    │         SC2219[style]: Instead of 'let expr', prefer (( expr )) .
    │         more info: https://www.shellcheck.net/wiki/SC2219
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Instead of 'let expr', prefer (( expr )) .
    ┌─ /Users/afrantz/workflows/tools/samtools.wdl:574:9
    │
574 │         let "n_cores -= 1"
    │         ^^^^^^^^^^^^^^^^^
    │         │
    │         SC2219[style]: Instead of 'let expr', prefer (( expr )) .
    │         more info: https://www.shellcheck.net/wiki/SC2219
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Since you double quoted this, it will not word split, and the loop will only run once.
    ┌─ /Users/afrantz/workflows/tools/samtools.wdl:577:21
    │
577 │         for file in ~{sep(" ", bams)}
    │                     ^^^^^^^^^^^^^^^^^
    │                     │
    │                     SC2066[error]: Since you double quoted this, it will not word split, and the loop will only run once.
    │                     more info: https://www.shellcheck.net/wiki/SC2066
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Double quote to prevent globbing and word splitting.
    ┌─ /Users/afrantz/workflows/tools/samtools.wdl:581:19
    │
581 │               ln -s $file
    │ ╭─────────────────────^
    │ │ ╭───────────────────'
582 │ │ │           bams+=" $(basename $file)"
    │ ╰─│─^ SC2086[info]: Double quote to prevent globbing and word splitting.
    │   ╰─' more info: https://www.shellcheck.net/wiki/SC2086
    │
    = fix: did you mean `"$file"`?

note[ShellCheck]: Double quote to prevent globbing and word splitting.
    ┌─ /Users/afrantz/workflows/tools/samtools.wdl:582:32
    │
582 │           bams+=" $(basename $file)"
    │                                ^^^^^
    │                                │
    │                                SC2086[info]: Double quote to prevent globbing and word splitting.
    │                                more info: https://www.shellcheck.net/wiki/SC2086
    │
    = fix: did you mean `"$file"`?

note[ShellCheck]: Double quote to prevent globbing and word splitting.
    ┌─ /Users/afrantz/workflows/tools/samtools.wdl:594:17
    │
594 │                 $bams
    │ ╭───────────────────^
    │ │ ╭─────────────────'
595 │ │ │     >>>
    │ ╰─│───^ SC2086[info]: Double quote to prevent globbing and word splitting.
    │   ╰───' more info: https://www.shellcheck.net/wiki/SC2086
    │
    = fix: did you mean `"$bams"`?

note[ShellCheck]: Instead of 'let expr', prefer (( expr )) .
    ┌─ /Users/afrantz/workflows/tools/samtools.wdl:670:9
    │
670 │         let "n_cores -= 1"
    │         ^^^^^^^^^^^^^^^^^
    │         │
    │         SC2219[style]: Instead of 'let expr', prefer (( expr )) .
    │         more info: https://www.shellcheck.net/wiki/SC2219
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Instead of 'let expr', prefer (( expr )) .
    ┌─ /Users/afrantz/workflows/tools/samtools.wdl:746:9
    │
746 │         let "n_cores -= 1"
    │         ^^^^^^^^^^^^^^^^^
    │         │
    │         SC2219[style]: Instead of 'let expr', prefer (( expr )) .
    │         more info: https://www.shellcheck.net/wiki/SC2219
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Instead of 'let expr', prefer (( expr )) .
    ┌─ /Users/afrantz/workflows/tools/samtools.wdl:871:9
    │
871 │         let "n_cores -= 1"
    │         ^^^^^^^^^^^^^^^^^
    │         │
    │         SC2219[style]: Instead of 'let expr', prefer (( expr )) .
    │         more info: https://www.shellcheck.net/wiki/SC2219
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Double quote to prevent globbing and word splitting.
    ┌─ /Users/afrantz/workflows/tools/samtools.wdl:934:30
    │
934 │         if [ -z "$(gunzip -c ~{prefix}*.fastq.gz | head -c 1 | tr '\0\n' __)" ]; then
    │                              ^^^^^^^^^
    │                              │
    │                              SC2086[info]: Double quote to prevent globbing and word splitting.
    │                              more info: https://www.shellcheck.net/wiki/SC2086
    │
    = fix: did you mean `"${WDLLbZ}"`?

note[ShellCheck]: Instead of 'let expr', prefer (( expr )) .
     ┌─ /Users/afrantz/workflows/tools/samtools.wdl:1039:9
     │
1039 │         let "n_cores -= 1"
     │         ^^^^^^^^^^^^^^^^^
     │         │
     │         SC2219[style]: Instead of 'let expr', prefer (( expr )) .
     │         more info: https://www.shellcheck.net/wiki/SC2219
     │
     = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Instead of 'let expr', prefer (( expr )) .
     ┌─ /Users/afrantz/workflows/tools/samtools.wdl:1132:9
     │
1132 │         let "n_cores -= 1"
     │         ^^^^^^^^^^^^^^^^^
     │         │
     │         SC2219[style]: Instead of 'let expr', prefer (( expr )) .
     │         more info: https://www.shellcheck.net/wiki/SC2219
     │
     = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Instead of 'let expr', prefer (( expr )) .
     ┌─ /Users/afrantz/workflows/tools/samtools.wdl:1254:9
     │
1254 │         let "n_cores -= 1"
     │         ^^^^^^^^^^^^^^^^^
     │         │
     │         SC2219[style]: Instead of 'let expr', prefer (( expr )) .
     │         more info: https://www.shellcheck.net/wiki/SC2219
     │
     = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Double quote to prevent globbing and word splitting.
     ┌─ /Users/afrantz/workflows/tools/samtools.wdl:1319:43
     │
1319 │         samtools faidx -o ~{outfile_name} $ref_fasta
     │                                           ^^^^^^^^^^
     │                                           │
     │                                           SC2086[info]: Double quote to prevent globbing and word splitting.
     │                                           more info: https://www.shellcheck.net/wiki/SC2086
     │
     = fix: did you mean `"$ref_fasta"`?

note[ShellCheck]: See if you can use ${variable//search/replace} instead.
    ┌─ /Users/afrantz/workflows/tools/util.wdl:132:9
    │
132 │         echo ~{string} | sed 's/~{delimiter}/\n/g' > split_strings.txt
    │         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    │         │
    │         SC2001[style]: See if you can use ${variable//search/replace} instead.
    │         more info: https://www.shellcheck.net/wiki/SC2001
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Double quote to prevent globbing and word splitting.
    ┌─ /Users/afrantz/workflows/tools/util.wdl:719:83
    │
719 │         TOTAL_READS=$(csvcut -t -c QualiMap_mqc-generalstats-qualimap-total_reads $gen_stats_file | tail -n 1 | awk '{ printf("%.0f", $1) }')
    │                                                                                   ^^^^^^^^^^^^^^^
    │                                                                                   │
    │                                                                                   SC2086[info]: Double quote to prevent globbing and word splitting.
    │                                                                                   more info: https://www.shellcheck.net/wiki/SC2086
    │
    = fix: did you mean `"$gen_stats_file"`?

note[ShellCheck]: Double quote to prevent globbing and word splitting.
    ┌─ /Users/afrantz/workflows/tools/util.wdl:720:94
    │
720 │         PERCENT_ALIGNED=$(csvcut -t -c QualiMap_mqc-generalstats-qualimap-percentage_aligned $gen_stats_file | tail -n 1 | awk '{ printf("%.3f", $1) }')
    │                                                                                              ^^^^^^^^^^^^^^^
    │                                                                                              │
    │                                                                                              SC2086[info]: Double quote to prevent globbing and word splitting.
    │                                                                                              more info: https://www.shellcheck.net/wiki/SC2086
    │
    = fix: did you mean `"$gen_stats_file"`?

note[ShellCheck]: Double quote to prevent globbing and word splitting.
    ┌─ /Users/afrantz/workflows/tools/util.wdl:721:87
    │
721 │         MEAN_COVERAGE=$(csvcut -t -c QualiMap_mqc-generalstats-qualimap-mean_coverage $gen_stats_file | tail -n 1 | awk '{ printf("%.3f", $1) }')
    │                                                                                       ^^^^^^^^^^^^^^^
    │                                                                                       │
    │                                                                                       SC2086[info]: Double quote to prevent globbing and word splitting.
    │                                                                                       more info: https://www.shellcheck.net/wiki/SC2086
    │
    = fix: did you mean `"$gen_stats_file"`?

note[ShellCheck]: Double quote to prevent globbing and word splitting.
    ┌─ /Users/afrantz/workflows/tools/util.wdl:722:90
    │
722 │         INSERT_SIZE=$(csvcut -t -c QualiMap_mqc-generalstats-qualimap-median_insert_size $gen_stats_file | tail -n 1)
    │                                                                                          ^^^^^^^^^^^^^^^
    │                                                                                          │
    │                                                                                          SC2086[info]: Double quote to prevent globbing and word splitting.
    │                                                                                          more info: https://www.shellcheck.net/wiki/SC2086
    │
    = fix: did you mean `"$gen_stats_file"`?

note[ShellCheck]: Double quote to prevent globbing and word splitting.
    ┌─ /Users/afrantz/workflows/tools/util.wdl:723:82
    │
723 │         MEAN_GC_CONTENT=$(csvcut -t -c QualiMap_mqc-generalstats-qualimap-avg_gc $gen_stats_file | tail -n 1 | awk '{ printf("%.3f", $1) }')
    │                                                                                  ^^^^^^^^^^^^^^^
    │                                                                                  │
    │                                                                                  SC2086[info]: Double quote to prevent globbing and word splitting.
    │                                                                                  more info: https://www.shellcheck.net/wiki/SC2086
    │
    = fix: did you mean `"$gen_stats_file"`?

note[ShellCheck]: Double quote to prevent globbing and word splitting.
    ┌─ /Users/afrantz/workflows/tools/util.wdl:724:93
    │
724 │         READ_LENGTH=$(csvcut -t -c ngsderive_mqc-generalstats-ngsderive-consensusreadlength $gen_stats_file | tail -n 1)
    │                                                                                             ^^^^^^^^^^^^^^^
    │                                                                                             │
    │                                                                                             SC2086[info]: Double quote to prevent globbing and word splitting.
    │                                                                                             more info: https://www.shellcheck.net/wiki/SC2086
    │
    = fix: did you mean `"$gen_stats_file"`?

note[ShellCheck]: Double quote to prevent globbing and word splitting.
    ┌─ /Users/afrantz/workflows/tools/util.wdl:725:81
    │
725 │         PLATFORM=$(csvcut -t -c ngsderive_mqc-generalstats-ngsderive-instrument $gen_stats_file | tail -n 1)
    │                                                                                 ^^^^^^^^^^^^^^^
    │                                                                                 │
    │                                                                                 SC2086[info]: Double quote to prevent globbing and word splitting.
    │                                                                                 more info: https://www.shellcheck.net/wiki/SC2086
    │
    = fix: did you mean `"$gen_stats_file"`?

note[ShellCheck]: Double quote to prevent globbing and word splitting.
    ┌─ /Users/afrantz/workflows/tools/util.wdl:727:83
    │
727 │         THIRTYX_PERCENT=$(csvcut -t -c QualiMap_mqc-generalstats-qualimap-30_x_pc $gen_stats_file | tail -n 1)
    │                                                                                   ^^^^^^^^^^^^^^^
    │                                                                                   │
    │                                                                                   SC2086[info]: Double quote to prevent globbing and word splitting.
    │                                                                                   more info: https://www.shellcheck.net/wiki/SC2086
    │
    = fix: did you mean `"$gen_stats_file"`?

note[ShellCheck]: Double quote to prevent globbing and word splitting.
    ┌─ /Users/afrantz/workflows/tools/util.wdl:728:86
    │
728 │         DUP_PERCENT=$(csvcut -t -c FastQC_mqc-generalstats-fastqc-percent_duplicates $gen_stats_file | tail -n 1)
    │                                                                                      ^^^^^^^^^^^^^^^
    │                                                                                      │
    │                                                                                      SC2086[info]: Double quote to prevent globbing and word splitting.
    │                                                                                      more info: https://www.shellcheck.net/wiki/SC2086
    │
    = fix: did you mean `"$gen_stats_file"`?

note[ShellCheck]: Double quote to prevent globbing and word splitting.
    ┌─ /Users/afrantz/workflows/tools/util.wdl:730:86
    │
730 │         STRANDEDNESS=$({ csvcut -t -c ngsderive_mqc-generalstats-ngsderive-predicted $gen_stats_file || echo "Not Applicable" ; } | tail -n 1)
    │                                                                                      ^^^^^^^^^^^^^^^
    │                                                                                      │
    │                                                                                      SC2086[info]: Double quote to prevent globbing and word splitting.
    │                                                                                      more info: https://www.shellcheck.net/wiki/SC2086
    │
    = fix: did you mean `"$gen_stats_file"`?

note[ShellCheck]: Instead of 'let expr', prefer (( expr )) .
    ┌─ /Users/afrantz/workflows/tools/util.wdl:806:9
    │
806 │         let "lines = ~{reads_per_file} * 4"
    │         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    │         │
    │         SC2219[style]: Instead of 'let expr', prefer (( expr )) .
    │         more info: https://www.shellcheck.net/wiki/SC2219
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Quote this to prevent word splitting.
    ┌─ /Users/afrantz/workflows/workflows/methylation/methylation-cohort.wdl:117:16
    │
117 │         python $(which combine.py) \
    │                ^^^^^^^^^^^^^^^^^^^
    │                │
    │                SC2046[warning]: Quote this to prevent word splitting.
    │                more info: https://www.shellcheck.net/wiki/SC2046
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Quote this to prevent word splitting.
    ┌─ /Users/afrantz/workflows/workflows/methylation/methylation-cohort.wdl:160:16
    │
160 │         python $(which filter.py) \
    │                ^^^^^^^^^^^^^^^^^^
    │                │
    │                SC2046[warning]: Quote this to prevent word splitting.
    │                more info: https://www.shellcheck.net/wiki/SC2046
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Quote this to prevent word splitting.
    ┌─ /Users/afrantz/workflows/workflows/methylation/methylation-cohort.wdl:202:16
    │
202 │         python $(which generate_umap.py) \
    │                ^^^^^^^^^^^^^^^^^^^^^^^^^
    │                │
    │                SC2046[warning]: Quote this to prevent word splitting.
    │                more info: https://www.shellcheck.net/wiki/SC2046
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Quote this to prevent word splitting.
    ┌─ /Users/afrantz/workflows/workflows/methylation/methylation-cohort.wdl:239:16
    │
239 │         python $(which plot_umap.py) --umap ~{umap} --output-name ~{plot_file}
    │                ^^^^^^^^^^^^^^^^^^^^^
    │                │
    │                SC2046[warning]: Quote this to prevent word splitting.
    │                more info: https://www.shellcheck.net/wiki/SC2046
    │
    = fix: address the diagnostic as recommended in the message

note[ShellCheck]: Quote this to prevent word splitting.
   ┌─ /Users/afrantz/workflows/workflows/methylation/methylation-preprocess.wdl:37:17
   │
37 │         Rscript $(which methylation-preprocess.R) \
   │                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
   │                 │
   │                 SC2046[warning]: Quote this to prevent word splitting.
   │                 more info: https://www.shellcheck.net/wiki/SC2046
   │
   = fix: address the diagnostic as recommended in the message

Included in the above are both true and false positives as well as some with the misplaced Span.

[a-frantz]

@thatRichman Just a poke in case you want to tackle this fix! No pressure though, one of us will get around to this eventually if you don't :)

[thatRichman]

Ooh yikes, happy to take a look!