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Added nf-test for gstama/collapse (#6301)
Co-authored-by: Simon Pearce <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| name: GSTAMA_COLLAPSE | ||
| name: gstama_collapse | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,49 @@ | ||
|
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| nextflow_process { | ||
|
|
||
| name "Test Process GSTAMA_COLLAPSE" | ||
| script "../main.nf" | ||
| process "GSTAMA_COLLAPSE" | ||
| config "./nextflow.config" | ||
|
|
||
| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "gstama" | ||
| tag "gstama/collapse" | ||
|
|
||
| test("test-gstama-collapse") { | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test' ], // meta map | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam', checkIfExists: true) | ||
| ] | ||
| input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome2.fasta', checkIfExists: true) | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot( | ||
| process.out.bed, | ||
| process.out.bed_trans_reads, | ||
| file(process.out.local_density_error[0][1]).readLines()[3..7], | ||
| file(process.out.polya[0][1]).readLines()[0], | ||
| file(process.out.read[0][1]).readLines()[3..7], | ||
| file(process.out.strand_check[0][1]).readLines()[0], | ||
| file(process.out.trans_report[0][1]).readLines()[3..7], | ||
| file(process.out.varcov[0][1]).readLines()[3..7], | ||
| file(process.out.variants[0][1]).readLines()[3..7], | ||
| process.out.versions | ||
| ).match() | ||
| } | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,67 @@ | ||
| { | ||
| "test-gstama-collapse": { | ||
| "content": [ | ||
| [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test_tc_collapsed.bed:md5,e5105198ed970a33ae0ecaa7bff421d9" | ||
| ] | ||
| ], | ||
| [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test_tc_trans_read.bed:md5,0ca1a32f33ef05242d897d913802554b" | ||
| ] | ||
| ], | ||
| [ | ||
| "m64014_190506_005857/1180161/ccs\tlde_pass\tchr22:16600000-16800000\t61141\t63656\t+\t1\t0\tna\tna\tna\tna\t1S23=1X5=2X4=1I4=3I7=1X6=1X2=1X3=1X1=2X9=1X1=1X18=1X14=1X8=1X35=1X10=1X16=1X2=1X15=1X11=1X21=1X10=1X31=1X16=1X5=1X9=1X8=1X7=1X12=2X13=2X32=1X7=1X8=1X1=1X1=1X7=1X8=1X3=1X4=1X1=1X12=1X5=1X10=1X5=2X4=2X17=1X9=1X1=1X4=1X2=1X19=1X3=1X1=1X7=2X3=1X7=1X9=1X3=1X3=1X17=1X8=1X1=1X8=1X17=1X6=1X17=1I5=1X10=1X33=1I5=1X5=1X46=1X35=1X9=1X18=1X3=1X15=2X16=1X85=1X2=1X21=1X15=1X68=1X64=1X66=1X26=1X25=1X5=1X11=2X53=1X23=1X1=1X4=1X10=1X17=1X11=1X17=1X12=1I2=1X29=1X3=1X16=1X50=1X9=1X9=1X1=1X9=1X3=1X74=1X4=1X2=1X3=1X7=1X2=1X11=1X4=1X1=1X51=2X18=1X36=1X53=3X84=1X22=1X30=1I52=1X24=1X19=1X22=2X5=1D1X8=1X16=1X6=1X4=1X13=1X27=1X77=1X51=1X47=1X31=1X18=1X25=1X14=1X34=1X6=19S", | ||
| "m64014_190506_005857/3868236/ccs\tlde_pass\tchr22:16600000-16800000\t62643\t66258\t+\t1\t0\tna\tna\tna\tna\t34=1X1=1X9=1X9=1X8=1X39=4D38=1X7=1X3=1X10=1X16=1X1=1X14=1X13=1X11=1X10=2X4=1X13=1X36=1X10=1X42=1X17=1X36=1X37=1X16=1X30=1I24=1X14=1X12=1X67=1X1=1D1=1X2=1D9=1X23=1X18=1X27=1X77=1X7=4D31=1X26=1X29=1X27=1X20=1X1=1X40=4D27=1X8=1X12=2X4=1X2=1X3=1X4=2X28=1X9=1X54=1X55=1X6=1X5=1X21=1X12=1X1=1X2=1X16=1X10=1X6=1X79=1X38=1X34=1X5=1X17=1X11=1X5=1X9=1X12=1X42=1X1=1X25=2X25=1X39=1X1=1X19=1X20=1X3=1X9=1X6=2X3=1X18=1X17=1X18=1X12=1X5=1X53=1X11=1X18=1X2=3D16=1X11=1I20=1X12=1X13=1X10=1X3=1X31=1X12=1X7=2X17=1X18=1X9=4D23=1X13=1X1=1X32=1X37=1X17=3X5=1X58=1X15=1X24=1X44=1I46=2X40=1X4=2I1X2=1X32=1X11=1X16=1X40=1X99=1X1=1X14=1X20=1X40=1X2=1X3=1X3=1X44=1X28=1X35=1X72=1X7=1X21=1X16=1X22=1X25=4D24=1X16=1X23=1X6=1X1=1X5=1X10=3D11=1X5=1X21=1X10=1X9=1X2=2I22=1X29=1X19=1X27=1X37=1X20=1X61=1X8=1X16=1X26=1X6=2X21=1X10=1X26=1X77=1X5=1X3=2X5=25S", | ||
| "m64014_190506_005857/1050667/ccs\tlde_pass\tchr22:16600000-16800000\t168385\t199436\t+\t2\t0\t0>0\t0,0,0,0,0>0,0,0,0,0\t0>0\t__________>__________\t16=1X20=1X19=1X58=1X40=1X7=1X12=1X2=1X41=1X93=1X48=1X5=1X4=1X40=1X10=1X27=2X25=1X2=1X4=1X24=1X7=2X14=1X52=1X5=1X6=2X8=1X21=1X4=1X35=1X40=1X75=1X3=1X21=1X20=1X23=2X31=1X19=1X27=1X3=1X52=1X40=1X10=1X28=1X34=1X33=1X26=1X13=1X56=2X31=2X11=1X94=1X41=1X1=1X20=1X32=1X10=1X64=1X4=1X39=2X6=2X15=1X63=1X28=1X34=1X33=1X7=1X3=1X17=1X20=1X47=1X7=2X11=1X2=1X5=1X6=1X41=1X7=1X77=1X14=1X35=1X14=1X32=1X52=1I10=1X30=1X9=1X36=1X2=1X66=1X4=1X38=1X5=1X12=1X19=1X75=1X26=2D11=1X20=1X3=1X1=1X14=1X20=1X7=1X14=1X24=1X2=1X25=1X4=1X81=1X15=1X15=1X27=2X17=28149N22=9S", | ||
| "m64014_190506_005857/6294364/ccs\tlde_pass\tchr22:16600000-16800000\t168536\t199436\t+\t2\t0\t1>0\t0,0,1,0,0>0,0,0,0,0\t4.T.A_3M>0\t_____X____>__________\t6=1X7=1X2=1X8=1D3=1X14=1X23=1X2=1X4=1X35=1X11=1X40=1X6=1X41=1X2=1X59=1X23=1X3=2X16=1X8=1X7=1X33=1X38=8I1=2I28=1X5=1X3=1X2=1X9=1X19=1X1=1X4=1X35=1X9=1X29=5D20=2D16=1X8=1X3=1X20=1X24=1X45=2X4=1I27=1X19=2X26=1X2=1X94=1X4=1X5=1X12=1X15=1X7=1X6=1X19=1X20=1X9=1I3=2X25=1X5=1X7=1X42=1X17=1X29=1X11=1X79=1X14=1X10=1X30=1X1=1X43=1X2=1X6=1X30=1I45=1X1=1I32=1X11=1X6=1X12=1X3=1X63=1X63=1X41=1X20=1X16=1I5=1X32=1I9=1X5=1X1=1I6=2X11=1X2=1X11=4D38=2X22=1X46=1X1=1I40=1X24=1X29=1X25=1X23=2X17=1X3=1X7=1X31=1X3=1X4=1X36=1X10=1X31=1D17=1X8=1X4=1X38=1X1=2X1=2X9=1X2=1X95=1X22=9D33=1X1=1X14=1X20=1X22=1X8=1X44=1X4=1X41=1X55=2X12=1X30=1X3=28161N24=7S", | ||
| "m64014_190506_005857/9307762/ccs\tlde_pass\tchr22:16600000-16800000\t169225\t199436\t+\t2\t0\t0>3\t0,0,0,0,0>2,0,1,0,0\t0>2M_2.A.C_1M_2I\t__________>__X_II____\t3S4=1X23=3X26=1X3=1X19=1X27=1X14=1X30=1X10=1X40=1X10=1X1=1X26=1X5=1X28=1X60=1X7=1X5=1X6=1X50=1X32=1X11=1X41=1X52=1X41=1X1=1X20=1X32=1X10=1X17=1X51=1X40=1X6=1X16=1X43=1X19=1X37=1X8=1X11=1X4=1X33=1X7=1X34=1X4=1X2=1X47=1X7=2X11=1X2=1X5=1X6=1X26=1X14=1X9=1X23=1X12=1X27=1X10=1X28=1X8=1X8=1X3=1X47=1X16=1X16=1X28=1X31=1X4=1X3=1X36=1X2=1X36=1X29=1X4=1X37=2X1=2X2=1X12=1X19=1X75=1X26=2D11=1X8=1X15=1X1=1X14=1X18=1X1=1X7=1X14=1X22=1X30=1X4=1X15=1X9=1X71=2X25=1X17=1X17=1X17=1X28=4D21=1X8=1X16=1X140=1X43=1X51=1X14=1X11=1X17=2X15=1X24=1X25=1X7=1X2=1X8=1X5=1X4=1X15=1X11=1X18=1D42=1X19=1X5=1X7=1X15=9D5=4D18=1X3=1X4=1X17=1X7=1X1=1X17=1X7=1X11=1X4=1X4=1X14=1X11=1X8=1X2=1X4=1X11=1X13=1X10=1X8=1X17=27297N2=1X1=2I22=8S" | ||
| ], | ||
| "cluster_id\ttrans_id\tstrand\ta_percent\ta_count\tsequence", | ||
| [ | ||
| "m64014_190506_005857/13631523/ccs\tchimeric\tchimeric\tNA\tNA\tNA\tNA\tNA", | ||
| "m64014_190506_005857/13238379/ccs\tforward_strand\tdiscarded\t7.53\t6.24\t0;3600;8;2;40\t3893\t2807S12=1X2=1D2=2X5=1X7=2X5=2I2=5I1X6=1X6=1X17=2X6=1X7=1X2=1X6=1X1=1X9=2X7=1X3=1X6=2X7=1X1=1X3=3030N1=2X12=1X17=2X4=1I7=1X5=1X8=1X25=1X5=1X2=1D8=1X12=1X1=2X9=2X7=793S", | ||
| "m64014_190506_005857/5048548/ccs\tnot_primary\tnot_primary\tNA\tNA\tNA\tNA\tNA", | ||
| "m64014_190506_005857/2491688/ccs\tchimeric\tchimeric\tNA\tNA\tNA\tNA\tNA", | ||
| "m64014_190506_005857/10945888/ccs\tnot_primary\tnot_primary\tNA\tNA\tNA\tNA\tNA" | ||
| ], | ||
| "read_id\tscaff_name\tstart_pos\tcigar\tstrands", | ||
| [ | ||
| "G1.3\t1\t99.21\t99.21\t92.96\t92.96\t0\t0\t0\t0\tna", | ||
| "G1.4\t1\t99.31\t99.31\t93.56\t93.56\t0\t0\t0\t0\tna", | ||
| "G1.5\t1\t99.69\t99.69\t95.46\t95.46\t0,0\t0,0\t0,0\t0,0\t0>0", | ||
| "G1.6\t1\t99.74\t99.74\t93.58\t93.58\t0,0\t0,0\t0,0\t0,0\t4.T.A_3M>0", | ||
| "G1.7\t1\t99.62\t99.62\t93.7\t93.7\t0,0\t0,0\t0,0\t0,0\t0>2M_2.A.C_1M_2I" | ||
| ], | ||
| [ | ||
| "chr22:16600000-16800000_6225\tm64014_190506_005857/11141276/ccs,m64014_190506_005857/13501955/ccs,m64014_190506_005857/13633438/ccs,m64014_190506_005857/6228265/ccs,m64014_190506_005857/7211438/ccs,m64014_190506_005857/8258125/ccs,m64014_190506_005857/9045622/ccs,m64014_190506_005857/9896837/ccs", | ||
| "chr22:16600000-16800000_6234\tm64014_190506_005857/10945789/ccs,m64014_190506_005857/11403968/ccs,m64014_190506_005857/13043967/ccs,m64014_190506_005857/13633438/ccs,m64014_190506_005857/6228265/ccs,m64014_190506_005857/9045622/ccs,m64014_190506_005857/9896837/ccs", | ||
| "chr22:16600000-16800000_6244\tm64014_190506_005857/10945789/ccs,m64014_190506_005857/11141276/ccs,m64014_190506_005857/11403968/ccs,m64014_190506_005857/13043967/ccs,m64014_190506_005857/13501955/ccs,m64014_190506_005857/13633438/ccs,m64014_190506_005857/3735911/ccs,m64014_190506_005857/6228265/ccs,m64014_190506_005857/8258125/ccs,m64014_190506_005857/8586246/ccs,m64014_190506_005857/9045622/ccs,m64014_190506_005857/9896837/ccs", | ||
| "chr22:16600000-16800000_6255\tm64014_190506_005857/11403968/ccs,m64014_190506_005857/13043967/ccs,m64014_190506_005857/13633438/ccs,m64014_190506_005857/3735911/ccs,m64014_190506_005857/7538257/ccs,m64014_190506_005857/8586246/ccs,m64014_190506_005857/9896837/ccs", | ||
| "chr22:16600000-16800000_6256\tm64014_190506_005857/11403968/ccs,m64014_190506_005857/13043967/ccs,m64014_190506_005857/13501955/ccs,m64014_190506_005857/13633438/ccs,m64014_190506_005857/3735911/ccs,m64014_190506_005857/7538257/ccs,m64014_190506_005857/8586246/ccs,m64014_190506_005857/9896837/ccs" | ||
| ], | ||
| [ | ||
| "chr22:16600000-16800000\t6225\tM\tT\tC\t8\t8\tm64014_190506_005857/9045622/ccs,m64014_190506_005857/8258125/ccs,m64014_190506_005857/11141276/ccs,m64014_190506_005857/6228265/ccs,m64014_190506_005857/9896837/ccs,m64014_190506_005857/13633438/ccs,m64014_190506_005857/7211438/ccs,m64014_190506_005857/13501955/ccs", | ||
| "chr22:16600000-16800000\t6234\tM\tG\tA\t5\t7\tm64014_190506_005857/9896837/ccs,m64014_190506_005857/6228265/ccs,m64014_190506_005857/13633438/ccs,m64014_190506_005857/13043967/ccs,m64014_190506_005857/9045622/ccs", | ||
| "chr22:16600000-16800000\t6244\tM\tC\tG\t11\t12\tm64014_190506_005857/9045622/ccs,m64014_190506_005857/8586246/ccs,m64014_190506_005857/11141276/ccs,m64014_190506_005857/6228265/ccs,m64014_190506_005857/13043967/ccs,m64014_190506_005857/9896837/ccs,m64014_190506_005857/13633438/ccs,m64014_190506_005857/8258125/ccs,m64014_190506_005857/10945789/ccs,m64014_190506_005857/3735911/ccs,m64014_190506_005857/13501955/ccs", | ||
| "chr22:16600000-16800000\t6255\tM\tT\tC\t7\t7\tm64014_190506_005857/7538257/ccs,m64014_190506_005857/8586246/ccs,m64014_190506_005857/13633438/ccs,m64014_190506_005857/11403968/ccs,m64014_190506_005857/9896837/ccs,m64014_190506_005857/13043967/ccs,m64014_190506_005857/3735911/ccs", | ||
| "chr22:16600000-16800000\t6256\tM\tG\tA\t7\t8\tm64014_190506_005857/7538257/ccs,m64014_190506_005857/8586246/ccs,m64014_190506_005857/13633438/ccs,m64014_190506_005857/11403968/ccs,m64014_190506_005857/9896837/ccs,m64014_190506_005857/13043967/ccs,m64014_190506_005857/3735911/ccs" | ||
| ], | ||
| [ | ||
| "versions.yml:md5,e78d77df56e6434d307e702b7875d005" | ||
| ] | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.8.4", | ||
| "nextflow": "24.04.4" | ||
| }, | ||
| "timestamp": "2024-08-26T10:53:08.268377" | ||
| } | ||
| } |
4 changes: 0 additions & 4 deletions
4
...s/nf-core/gstama/collapse/nextflow.config → ...ore/gstama/collapse/tests/nextflow.config
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,10 +1,6 @@ | ||
| process { | ||
|
|
||
| publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } | ||
|
|
||
| withName: GSTAMA_COLLAPSE { | ||
| ext.args = '-x capped -b BAM' | ||
| ext.prefix = { "${meta.id}_tc" } | ||
| } | ||
|
|
||
| } |
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