# Use inline javascript when specifying input string **URL:** \ **Category:** CWL Questions\ **Created:** [November 26, 2024, 5:55pm UTC](https://cwl.discourse.group/t/use-inline-javascript-when-specifying-input-string/963 "2024-11-26T17:55:53Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![skgo](https://avatars.discourse-cdn.com/v4/letter/s/7cd45c/32.png) [@skgo](https://cwl.discourse.group/u/skgo)\ **Post date:** [November 26, 2024, 5:55pm UTC](https://cwl.discourse.group/t/use-inline-javascript-when-specifying-input-string/963/1 "2024-11-26T17:55:53Z")
Is it possible to use inline javascript in order to construct an input string in a workflow? Below is an example of my workflow: ```auto cwlVersion: v1.2 class: Workflow requirements: InlineJavascriptRequirement: {} inputs: sampleID: type: string fastq1: type: File fastq2: type: File library: type: string platform: type: string platformUnit: type: string outputs: out: type: File outputSource: GATK_AddOrReplaceReadGroups/output_bam steps: GATK_FastqToSam: run: ../../tools/GATK/GATK_FastqToSam.cwl in: fastq1: fastq1 fastq2: fastq2 output: $(inputs.sampleID + ".bam") SM: sampleID out: [output_bam] GATK_AddOrReplaceReadGroups: run: ../../tools/GATK/GATK_AddOrReplaceReadGroups.cwl in: bam: source: GATK_FastqToSam/output_bam output: $(inputs.sampleID + ".RG.bam") SM: sampleID LB: library PL: platform PU: platformUnit out: [output_bam] ``` Specifically, when specifying the input parameter named “output” I would like to concatenate the sampleID string to another string. You can see I’ve tried to do it like so ```auto output: $(inputs.sampleID + ".RG.bam") ``` However, cwltool gives me the following error: ```auto ERROR Tool definition failed validation: convert_fastq_to_bam.cwl:27:1: checking field 'steps' convert_fastq_to_bam.cwl:36:3: checking object 'convert_fastq_to_bam.cwl#GATK_AddOrReplaceReadGroups' convert_fastq_to_bam.cwl:38:5: checking field 'in' convert_fastq_to_bam.cwl:41:7: checking object 'convert_fastq_to_bam.cwl#GATK_AddOrReplaceReadGroups/output' Field 'source' references unknown identifier '$(inputs.sampleID + ".RG.bam")', tried file:///Users/me/Documents/cwl-demo-pipeline/workflows/alignment/convert_fastq_to_bam.cwl#$(inputs.sampleID + ".RG.bam") ``` ---
**Author:** ![tetron](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/tetron/32/40_2.png) [@tetron](https://cwl.discourse.group/u/tetron)\ **Post date:** [November 27, 2024, 3:17pm UTC](https://cwl.discourse.group/t/use-inline-javascript-when-specifying-input-string/963/2 "2024-11-27T15:17:06Z")
> [@skgo](#): > > ```auto > GATK_FastqToSam: > run: ../../tools/GATK/GATK_FastqToSam.cwl > in: > fastq1: fastq1 > fastq2: fastq2 > output: $(inputs.sampleID + ".bam") > SM: sampleID > out: [output_bam] > > ``` Yes, you want to do this: ```auto output: { valueFrom: '$(inputs.sampleID + ".bam")' } ``` ---
**Author:** ![mrc](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/mrc/32/3_2.png) [@mrc](https://cwl.discourse.group/u/mrc)\ **Post date:** [November 27, 2024, 3:49pm UTC](https://cwl.discourse.group/t/use-inline-javascript-when-specifying-input-string/963/3 "2024-11-27T15:49:51Z")
> [@tetron](#): > > ` output: { valueFrom: '$(inputs.sampleID + ".bam")' }` Or even more concisely ` output: { valueFrom: $(inputs.sampleID).bam }` ---
**Author:** ![tetron](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/tetron/32/40_2.png) [@tetron](https://cwl.discourse.group/u/tetron)\ **Post date:** [November 27, 2024, 4:03pm UTC](https://cwl.discourse.group/t/use-inline-javascript-when-specifying-input-string/963/4 "2024-11-27T16:03:09Z")
> [@mrc](#): > > Or even more concisely ` output: { valueFrom: $(inputs.sampleID).bam } Michael meant to write: `output: { valueFrom: $(inputs.sampleID).bam }` Michael’s version is actually much better, as it is a plain parameter substitution and avoids doing any Javascript evaluation at all. ---
**Author:** ![skgo](https://avatars.discourse-cdn.com/v4/letter/s/7cd45c/32.png) [@skgo](https://cwl.discourse.group/u/skgo)\ **Post date:** [December 3, 2024, 4:52pm UTC](https://cwl.discourse.group/t/use-inline-javascript-when-specifying-input-string/963/5 "2024-12-03T16:52:05Z")
Thank you for your help. I’m trying to run my workflow with the following command: ```auto cwltool convert_fastq_to_bam.cwl --fastq1 ../../test_data/mysample_R1_001.fastq.gz --fastq2 ../../test_data/mysample_R2_001.fastq.gz --library "Solexa-272222" --platform "illumina" --platformUnit "H0164ALXX140820.2" --sampleID "mysample" ``` but am getting this error: ```auto INFO [workflow] start INFO [workflow] starting step GATK_FastqToSam Expecting value: line 1 column 1 (char 0) script was: 01 "use strict"; 02 var inputs = { 03 "SM": "mysample", 04 "fastq1": { 05 "class": "File", 06 "location": "file:///Users/me/Documents/projects/cwl-demo-pipeline/test_data/mysample_R1_001.fastq.gz", 07 "size": 70944943, 08 "basename": "mysample_R1_001.fastq.gz", 09 "nameroot": "mysample_R1_001.fastq", 10 "nameext": ".gz" 11 }, 12 "fastq2": { 13 "class": "File", 14 "location": "file:///Users/me/Documents/projects/cwl-demo-pipeline/test_data/mysample_R2_001.fastq.gz", 15 "size": 77256188, 16 "basename": "mysample_R2_001.fastq.gz", 17 "nameroot": "mysample_R2_001.fastq", 18 "nameext": ".gz" 19 }, 20 "output": null 21 }; 22 var self = null; 23 var runtime = { 24 "tmpdir": null, 25 "outdir": null 26 }; 27 (function(){return ((inputs.sampleID));})() stdout was: 'undefined' stderr was: '' ``` Below is what my workflow currently looks like: ```auto cwlVersion: v1.2 class: Workflow requirements: InlineJavascriptRequirement: {} StepInputExpressionRequirement: {} inputs: sampleID: type: string fastq1: type: File fastq2: type: File library: type: string platform: type: string platformUnit: type: string outputs: out: type: File outputSource: GATK_AddOrReplaceReadGroups/output_bam steps: GATK_FastqToSam: run: ../../tools/GATK/GATK_FastqToSam.cwl in: fastq1: fastq1 fastq2: fastq2 output: { valueFrom: $(inputs.sampleID).bam } SM: sampleID out: [output_bam] GATK_AddOrReplaceReadGroups: run: ../../tools/GATK/GATK_AddOrReplaceReadGroups.cwl in: bam: source: GATK_FastqToSam/output_bam output: { valueFrom: $(inputs.sampleID).RG.bam } SM: sampleID LB: library PL: platform PU: platformUnit out: [output_bam] ``` Is there something I’m overlooking? edit: For what it’s worth, tetron’s original answer runs but produces `undefined.bam` as the value of `output`. ---
**Author:** ![mrc](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/mrc/32/3_2.png) [@mrc](https://cwl.discourse.group/u/mrc)\ **Post date:** [December 3, 2024, 5:06pm UTC](https://cwl.discourse.group/t/use-inline-javascript-when-specifying-input-string/963/6 "2024-12-03T17:06:04Z")
> [@tetron](#): > > output: { valueFrom: $(inputs.sampleID).bam } Try `output: { valueFrom: $(inputs.SM).bam }`