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feat: can_be_line_broken is exhaustive
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@a-frantz
a-frantz committed Jan 15, 2025
1 parent 6bf613f commit 9fb4691
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Showing 3 changed files with 132 additions and 92 deletions.
26 changes: 24 additions & 2 deletions wdl-format/src/token/post.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -149,11 +149,33 @@ fn can_be_line_broken(kind: SyntaxKind) -> Option<LineBreak> {
| SyntaxKind::CloseBracket
| SyntaxKind::CloseParen
| SyntaxKind::CloseHeredoc
| SyntaxKind::Assignment => Some(LineBreak::Before),
| SyntaxKind::Assignment
| SyntaxKind::Plus
| SyntaxKind::Minus
| SyntaxKind::Asterisk
| SyntaxKind::Slash
| SyntaxKind::Percent
| SyntaxKind::Exponentiation
| SyntaxKind::Equal
| SyntaxKind::NotEqual
| SyntaxKind::Less
| SyntaxKind::LessEqual
| SyntaxKind::Greater
| SyntaxKind::GreaterEqual
| SyntaxKind::LogicalAnd
| SyntaxKind::LogicalOr
| SyntaxKind::AfterKeyword
| SyntaxKind::AsKeyword
| SyntaxKind::IfKeyword
| SyntaxKind::ElseKeyword
| SyntaxKind::ThenKeyword => Some(LineBreak::Before),
SyntaxKind::OpenBrace
| SyntaxKind::OpenBracket
| SyntaxKind::OpenParen
| SyntaxKind::OpenHeredoc => Some(LineBreak::After),
| SyntaxKind::OpenHeredoc
| SyntaxKind::Colon
| SyntaxKind::PlaceholderOpen
| SyntaxKind::Comma => Some(LineBreak::After),
_ => None,
}
}
Expand Down
100 changes: 59 additions & 41 deletions wdl-format/tests/format/ENCODE-DCC_chip-seq-pipeline/source.formatted.wdl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1103,7 +1103,8 @@ workflow chip {
])
String peak_type_ = if peak_caller_ == "spp" then "regionPeak" else "narrowPeak"
Boolean enable_idr = pipeline_type == "tf" # enable_idr for TF chipseq only
String idr_rank_ = if peak_caller_ == "spp" then "signal.value" else if peak_caller_ == "macs2" then "p.value" else "p.value"
String idr_rank_ = if peak_caller_ == "spp" then "signal.value" else if peak_caller_
== "macs2" then "p.value" else "p.value"
Int cap_num_peak_spp = 300000
Int cap_num_peak_macs2 = 500000
Int cap_num_peak_ = if peak_caller_ == "spp" then select_first([
Expand All @@ -1121,9 +1122,12 @@ workflow chip {
Boolean align_only_ = if pipeline_type == "control" then true else align_only
Float align_mem_factor_ = if aligner_ == "bowtie2" then align_bowtie2_mem_factor else align_bwa_mem_factor
Float align_disk_factor_ = if aligner_ == "bowtie2" then align_bowtie2_disk_factor else align_bwa_disk_factor
Float call_peak_mem_factor_ = if peak_caller_ == "spp" then call_peak_spp_mem_factor else call_peak_macs2_mem_factor
Float call_peak_disk_factor_ = if peak_caller_ == "spp" then call_peak_spp_disk_factor else call_peak_macs2_disk_factor
Float align_disk_factor_ = if aligner_ == "bowtie2" then align_bowtie2_disk_factor
else align_bwa_disk_factor
Float call_peak_mem_factor_ = if peak_caller_ == "spp" then call_peak_spp_mem_factor
else call_peak_macs2_mem_factor
Float call_peak_disk_factor_ = if peak_caller_ == "spp" then call_peak_spp_disk_factor
else call_peak_macs2_disk_factor
# temporary 2-dim fastqs array [rep_id][merge_id]
Array[Array[File]] fastqs_R1 = if length(fastqs_rep10_R1) > 0 then [
Expand Down Expand Up @@ -1321,8 +1325,8 @@ workflow chip {
runtime_environment = runtime_environment,
}
}
if ((num_rep_fastq > 0 || num_ctl_fastq > 0) && aligner_ != "bwa" && aligner_ != "bowtie2" && aligner_ != "custom"
) {
if ((num_rep_fastq > 0 || num_ctl_fastq > 0) && aligner_ != "bwa" && aligner_ != "bowtie2"
&& aligner_ != "custom") {
call raise_exception as error_wrong_aligner { input:
msg = "Choose chip.aligner to align your fastqs. Choices: bwa, bowtie2, custom.",
runtime_environment = runtime_environment,
Expand Down Expand Up @@ -1351,7 +1355,11 @@ workflow chip {
if ((ctl_depth_limit > 0 || exp_ctl_depth_ratio_limit > 0) && num_ctl > 1 && length(
ctl_paired_ends) > 1) {
call raise_exception as error_subsample_pooled_control_with_mixed_endedness { input:
msg = "Cannot use automatic control subsampling (\"chip.ctl_depth_limit\">0 and \"chip.exp_ctl_depth_limit\">0) for " + "multiple controls with mixed endedness (e.g. SE ctl-rep1 and PE ctl-rep2). " + "Automatic control subsampling is enabled by default. " + "Disable automatic control subsampling by explicitly defining the above two parameters as 0 in your input JSON file. " + "You can still use manual control subsamping (\"chip.ctl_subsample_reads\">0) since it is done " + "for individual control's TAG-ALIGN output according to each control's endedness. ",
msg = "Cannot use automatic control subsampling (\"chip.ctl_depth_limit\">0 and \"chip.exp_ctl_depth_limit\">0) for "
+ "multiple controls with mixed endedness (e.g. SE ctl-rep1 and PE ctl-rep2). "
+ "Automatic control subsampling is enabled by default. " + "Disable automatic control subsampling by explicitly defining the above two parameters as 0 in your input JSON file. "
+ "You can still use manual control subsamping (\"chip.ctl_subsample_reads\">0) since it is done "
+ "for individual control's TAG-ALIGN output according to each control's endedness. ",
runtime_environment = runtime_environment,
}
}
Expand Down Expand Up @@ -1390,7 +1398,8 @@ workflow chip {
aligner = aligner_,
mito_chr_name = mito_chr_name_,
custom_align_py = custom_align_py,
idx_tar = if aligner == "bwa" then bwa_idx_tar_ else if aligner == "bowtie2" then bowtie2_idx_tar_ else custom_aligner_idx_tar,
idx_tar = if aligner == "bwa" then bwa_idx_tar_ else if aligner == "bowtie2"
then bowtie2_idx_tar_ else custom_aligner_idx_tar,
paired_end = paired_end_,
use_bwa_mem_for_pe = use_bwa_mem_for_pe,
bwa_mem_read_len_limit = bwa_mem_read_len_limit,
Expand Down Expand Up @@ -1496,7 +1505,8 @@ workflow chip {
aligner = aligner_,
mito_chr_name = mito_chr_name_,
custom_align_py = custom_align_py,
idx_tar = if aligner == "bwa" then bwa_idx_tar_ else if aligner == "bowtie2" then bowtie2_idx_tar_ else custom_aligner_idx_tar,
idx_tar = if aligner == "bwa" then bwa_idx_tar_ else if aligner == "bowtie2"
then bowtie2_idx_tar_ else custom_aligner_idx_tar,
paired_end = false,
use_bwa_mem_for_pe = false,
bwa_mem_read_len_limit = 0,
Expand Down Expand Up @@ -1543,8 +1553,8 @@ workflow chip {
}
# special trimming/mapping for xcor (when starting from BAMs)
Boolean has_input_of_bam2ta_no_dedup = (has_output_of_align || defined(align.bam)) && !defined(
bam2ta_no_dedup_R1.ta)
Boolean has_input_of_bam2ta_no_dedup = (has_output_of_align || defined(align.bam))
&& !defined(bam2ta_no_dedup_R1.ta)
if (has_input_of_bam2ta_no_dedup) {
call filter as filter_no_dedup { input:
bam = bam_,
Expand Down Expand Up @@ -1582,8 +1592,8 @@ workflow chip {
# if not starting from fastqs, keep using old method
# (mapping with both ends for tag-aligns to be used for xcor)
# subsample tagalign (non-mito) and cross-correlation analysis
File? ta_xcor = if defined(bam2ta_no_dedup_R1.ta) then bam2ta_no_dedup_R1.ta else if defined(
bam2ta_no_dedup.ta) then bam2ta_no_dedup.ta else ta_
File? ta_xcor = if defined(bam2ta_no_dedup_R1.ta) then bam2ta_no_dedup_R1.ta else
if defined(bam2ta_no_dedup.ta) then bam2ta_no_dedup.ta else ta_
Boolean paired_end_xcor = if defined(bam2ta_no_dedup_R1.ta) then false else paired_end_
Boolean has_input_of_xcor = defined(ta_xcor)
Expand Down Expand Up @@ -1633,7 +1643,8 @@ workflow chip {
aligner = aligner_,
mito_chr_name = mito_chr_name_,
custom_align_py = custom_align_py,
idx_tar = if aligner == "bwa" then bwa_idx_tar_ else if aligner == "bowtie2" then bowtie2_idx_tar_ else custom_aligner_idx_tar,
idx_tar = if aligner == "bwa" then bwa_idx_tar_ else if aligner == "bowtie2"
then bowtie2_idx_tar_ else custom_aligner_idx_tar,
paired_end = ctl_paired_end_,
use_bwa_mem_for_pe = use_bwa_mem_for_pe,
bwa_mem_read_len_limit = bwa_mem_read_len_limit,
Expand Down Expand Up @@ -1802,8 +1813,8 @@ workflow chip {
[
choose_ctl.chosen_ctl_ta_subsample,
])[i] else 0
Boolean chosen_ctl_paired_end = if chosen_ctl_ta_id == -2 then false else if chosen_ctl_ta_id == -1 then ctl_paired_end_[
0] else ctl_paired_end_[chosen_ctl_ta_id]
Boolean chosen_ctl_paired_end = if chosen_ctl_ta_id == -2 then false else if chosen_ctl_ta_id
== -1 then ctl_paired_end_[0] else ctl_paired_end_[chosen_ctl_ta_id]

if (chosen_ctl_ta_id > -2 && chosen_ctl_ta_subsample > 0) {
call subsample_ctl { input:
Expand All @@ -1816,7 +1827,8 @@ workflow chip {
runtime_environment = runtime_environment,
}
}
Array[File] chosen_ctl_tas = if chosen_ctl_ta_id <= -2 then [] else if chosen_ctl_ta_subsample > 0 then [
Array[File] chosen_ctl_tas = if chosen_ctl_ta_id <= -2 then [] else if chosen_ctl_ta_subsample
> 0 then [
select_first([
subsample_ctl.ta_subsampled,
]),
Expand All @@ -1830,8 +1842,8 @@ workflow chip {
]),
]
}
Int chosen_ctl_ta_pooled_subsample = if has_all_input_of_choose_ctl && !align_only_ then select_first(
[
Int chosen_ctl_ta_pooled_subsample = if has_all_input_of_choose_ctl && !align_only_
then select_first([
choose_ctl.chosen_ctl_ta_subsample_pooled,
]) else 0
Expand Down Expand Up @@ -1865,7 +1877,8 @@ workflow chip {
mem_factor = call_peak_mem_factor_,
disk_factor = call_peak_disk_factor_,
time_hr = call_peak_time_hr,
runtime_environment = if peak_caller_ == "spp" then runtime_environment_spp else if peak_caller_ == "macs2" then runtime_environment_macs2 else runtime_environment,
runtime_environment = if peak_caller_ == "spp" then runtime_environment_spp
else if peak_caller_ == "macs2" then runtime_environment_macs2 else runtime_environment,
}
}
File? peak_ = if has_output_of_call_peak then peaks[i] else call_peak.peak
Expand Down Expand Up @@ -1917,7 +1930,8 @@ workflow chip {
mem_factor = call_peak_mem_factor_,
disk_factor = call_peak_disk_factor_,
time_hr = call_peak_time_hr,
runtime_environment = if peak_caller_ == "spp" then runtime_environment_spp else if peak_caller_ == "macs2" then runtime_environment_macs2 else runtime_environment,
runtime_environment = if peak_caller_ == "spp" then runtime_environment_spp
else if peak_caller_ == "macs2" then runtime_environment_macs2 else runtime_environment,
}
}
File? peak_pr1_ = if has_output_of_call_peak_pr1 then peaks_pr1[i] else call_peak_pr1.peak
Expand Down Expand Up @@ -1948,7 +1962,8 @@ workflow chip {
mem_factor = call_peak_mem_factor_,
disk_factor = call_peak_disk_factor_,
time_hr = call_peak_time_hr,
runtime_environment = if peak_caller_ == "spp" then runtime_environment_spp else if peak_caller_ == "macs2" then runtime_environment_macs2 else runtime_environment,
runtime_environment = if peak_caller_ == "spp" then runtime_environment_spp
else if peak_caller_ == "macs2" then runtime_environment_macs2 else runtime_environment,
}
}
File? peak_pr2_ = if has_output_of_call_peak_pr2 then peaks_pr2[i] else call_peak_pr2.peak
Expand All @@ -1975,8 +1990,8 @@ workflow chip {
}
}
# actually not an array
Array[File?] chosen_ctl_ta_pooled = if !has_all_input_of_choose_ctl || align_only_ then [
] else if chosen_ctl_ta_pooled_subsample > 0 then [
Array[File?] chosen_ctl_ta_pooled = if !has_all_input_of_choose_ctl || align_only_
then [] else if chosen_ctl_ta_pooled_subsample > 0 then [
subsample_ctl_pooled.ta_subsampled,
] else if num_ctl < 2 then [
ctl_ta_[0],
Expand All @@ -1986,8 +2001,8 @@ workflow chip {
Boolean has_input_of_call_peak_pooled = defined(pool_ta.ta_pooled)
Boolean has_output_of_call_peak_pooled = defined(peak_pooled)
if (has_input_of_call_peak_pooled && !has_output_of_call_peak_pooled && !align_only_ && num_rep > 1
) {
if (has_input_of_call_peak_pooled && !has_output_of_call_peak_pooled && !align_only_
&& num_rep > 1) {
# call peaks on pooled replicate
# always call peaks for pooled replicate to get signal tracks
call call_peak as call_peak_pooled { input:
Expand All @@ -2012,7 +2027,8 @@ workflow chip {
mem_factor = call_peak_mem_factor_,
disk_factor = call_peak_disk_factor_,
time_hr = call_peak_time_hr,
runtime_environment = if peak_caller_ == "spp" then runtime_environment_spp else if peak_caller_ == "macs2" then runtime_environment_macs2 else runtime_environment,
runtime_environment = if peak_caller_ == "spp" then runtime_environment_spp
else if peak_caller_ == "macs2" then runtime_environment_macs2 else runtime_environment,
}
}
File? peak_pooled_ = if has_output_of_call_peak_pooled then peak_pooled else call_peak_pooled.peak
Expand Down Expand Up @@ -2040,8 +2056,8 @@ workflow chip {
Boolean has_input_of_call_peak_ppr1 = defined(pool_ta_pr1.ta_pooled)
Boolean has_output_of_call_peak_ppr1 = defined(peak_ppr1)
if (has_input_of_call_peak_ppr1 && !has_output_of_call_peak_ppr1 && !align_only_ && !true_rep_only && num_rep > 1
) {
if (has_input_of_call_peak_ppr1 && !has_output_of_call_peak_ppr1 && !align_only_ && !true_rep_only
&& num_rep > 1) {
# call peaks on 1st pooled pseudo replicates
call call_peak as call_peak_ppr1 { input:
peak_caller = peak_caller_,
Expand All @@ -2065,15 +2081,16 @@ workflow chip {
mem_factor = call_peak_mem_factor_,
disk_factor = call_peak_disk_factor_,
time_hr = call_peak_time_hr,
runtime_environment = if peak_caller_ == "spp" then runtime_environment_spp else if peak_caller_ == "macs2" then runtime_environment_macs2 else runtime_environment,
runtime_environment = if peak_caller_ == "spp" then runtime_environment_spp
else if peak_caller_ == "macs2" then runtime_environment_macs2 else runtime_environment,
}
}
File? peak_ppr1_ = if has_output_of_call_peak_ppr1 then peak_ppr1 else call_peak_ppr1.peak
Boolean has_input_of_call_peak_ppr2 = defined(pool_ta_pr2.ta_pooled)
Boolean has_output_of_call_peak_ppr2 = defined(peak_ppr2)
if (has_input_of_call_peak_ppr2 && !has_output_of_call_peak_ppr2 && !align_only_ && !true_rep_only && num_rep > 1
) {
if (has_input_of_call_peak_ppr2 && !has_output_of_call_peak_ppr2 && !align_only_ && !true_rep_only
&& num_rep > 1) {
# call peaks on 2nd pooled pseudo replicates
call call_peak as call_peak_ppr2 { input:
peak_caller = peak_caller_,
Expand All @@ -2097,7 +2114,8 @@ workflow chip {
mem_factor = call_peak_mem_factor_,
disk_factor = call_peak_disk_factor_,
time_hr = call_peak_time_hr,
runtime_environment = if peak_caller_ == "spp" then runtime_environment_spp else if peak_caller_ == "macs2" then runtime_environment_macs2 else runtime_environment,
runtime_environment = if peak_caller_ == "spp" then runtime_environment_spp
else if peak_caller_ == "macs2" then runtime_environment_macs2 else runtime_environment,
}
}
File? peak_ppr2_ = if has_output_of_call_peak_ppr2 then peak_ppr2 else call_peak_ppr2.peak
Expand Down Expand Up @@ -2417,8 +2435,8 @@ task align {
~{"--phred-score-format " + trimmomatic_phred_score_format} \
--out-dir-R1 R1$NEW_SUFFIX \
~{if paired_end then "--out-dir-R2 R2$NEW_SUFFIX" else ""} \
~{"--trimmomatic-java-heap " + if defined(trimmomatic_java_heap) then trimmomatic_java_heap else (
round(mem_gb * trimmomatic_java_heap_factor) + "G")} \
~{"--trimmomatic-java-heap " + if defined(trimmomatic_java_heap) then trimmomatic_java_heap
else (round(mem_gb * trimmomatic_java_heap_factor) + "G")} \
~{"--nth " + cpu}
SUFFIX=$NEW_SUFFIX
fi
Expand Down Expand Up @@ -2522,8 +2540,8 @@ task filter {
~{"--mito-chr-name " + mito_chr_name} \
~{"--mem-gb " + samtools_mem_gb} \
~{"--nth " + cpu} \
~{"--picard-java-heap " + if defined(picard_java_heap) then picard_java_heap else (
round(mem_gb * picard_java_heap_factor) + "G")}
~{"--picard-java-heap " + if defined(picard_java_heap) then picard_java_heap
else (round(mem_gb * picard_java_heap_factor) + "G")}
if [ '~{redact_nodup_bam}' == 'true' ]; then
python3 $(which encode_task_bam_to_pbam.py) \
Expand Down Expand Up @@ -3196,8 +3214,8 @@ task gc_bias {
python3 $(which encode_task_gc_bias.py) \
~{"--nodup-bam " + nodup_bam} \
~{"--ref-fa " + ref_fa} \
~{"--picard-java-heap " + if defined(picard_java_heap) then picard_java_heap else (
round(mem_gb * picard_java_heap_factor) + "G")}
~{"--picard-java-heap " + if defined(picard_java_heap) then picard_java_heap
else (round(mem_gb * picard_java_heap_factor) + "G")}
>>>
output {
Expand Down Expand Up @@ -3403,8 +3421,8 @@ task read_genome_tsv {
)
String? mito_chr_name = if size("mito_chr_name") == 0 then null_s else read_string(
"mito_chr_name")
String? regex_bfilt_peak_chr_name = if size("regex_bfilt_peak_chr_name") == 0 then "chr[\\dXY]+" else read_string(
"regex_bfilt_peak_chr_name")
String? regex_bfilt_peak_chr_name = if size("regex_bfilt_peak_chr_name") == 0 then "chr[\\dXY]+"
else read_string("regex_bfilt_peak_chr_name")
}

runtime {
Expand Down
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