Compare revisions

Heinrich Lukas Weil · Heinrich Lukas Weil · Caroline Ott · Caroline Ott · Caroline Ott · Heinrich Lukas Weil
--- a/assays/measurement1/isa.assay.xlsx
+++ b/assays/measurement1/isa.assay.xlsx
--- a/assays/measurement1/isa.datamap.xlsx
+++ b/assays/measurement1/isa.datamap.xlsx
--- a/assays/measurement2/isa.assay.xlsx
+++ b/assays/measurement2/isa.assay.xlsx
--- a/isa.investigation.xlsx
+++ b/isa.investigation.xlsx
--- a/runs/fsResult1/result.csv
+++ b/runs/fsResult1/result.csv
--- a/runs/ARCMountResult/run.cwl
+++ b/runs/ARCMountResult/run.cwl
+cwlVersion: v1.2
+class: Workflow
+
+requirements:
+  MultipleInputFeatureRequirement: {}
+
+inputs:
+  arcDirectory: Directory
+
+steps:
+  ARCMount:
+    run: ../../workflows/ARCMount/workflow.cwl
+    in:
+      arcDirectory: arcDirectory
+    out: [output]
+
+outputs:
+  ARCMountResult:
+    type: File
+    outputSource: ARCMount/output
\ No newline at end of file
--- a/runs/ARCMountResult/run.yml
+++ b/runs/ARCMountResult/run.yml
+arcDirectory:
+  class: Directory
+  path: ../../
+
+arc:performer:
+  - class: arc:Person
+    arc:first name: "Caroline"
+    arc:last name: "Ott"
+    arc:email: "ottj@rptu.de"
+    arc:affiliation: "RPTU Kaiserslautern/Landau"
+
+$namespaces:
+  arc: https://github.com/nfdi4plants/ARC_ontology
+
+$schemas:
+  - https://raw.githubusercontent.com/nfdi4plants/ARC_ontology/main/ARC_v2.0.owl
--- a/runs/DevcontainerResult/result.csv
+++ b/runs/DevcontainerResult/result.csv
+Sum_1-2
+52.374927
+30.708113
+43.347295
+32.330910
+68.832634
+50.943254
+82.709457
+45.815823
+49.329293
+15.044567
+42.581675
+61.490285
+61.483285
+33.515325
+39.027573
+57.814962
+41.484288
+62.969456
+56.084297
+76.014723
+39.715133
+73.319637
+67.026630
+56.888570
+48.411011
+70.181930
+18.055983
+35.218257
+26.840155
+72.385753
+43.972671
+44.078586
+53.938409
+43.395488
+28.723837
+54.061480
+58.528494
+52.236839
+56.893014
+56.525366
+58.955729
+46.444395
+39.269410
+44.423325
+19.510763
+48.672524
+64.933334
+60.750569
+45.516685
+46.623334
+76.270554
+29.934011
+50.275506
+40.572500
+55.508817
+43.844585
+57.298854
+38.721723
+49.707433
+48.383707
+73.873611
+56.579798
+49.573657
+74.940937
+48.889656
+11.609634
+39.675693
+29.804500
+43.964936
+35.057027
+37.625311
+77.481503
+41.714170
+52.904955
+35.366910
+39.166247
+53.024085
+7.132227
+54.059714
+38.487312
+79.778612
+49.592970
+42.861946
+63.583801
+81.084601
+29.562834
+54.967924
+56.813437
+50.634788
+45.835761
+53.669806
+27.804082
+62.293055
+42.933661
+34.954878
+64.885836
+57.539051
+33.539328
+69.979137
+28.013399
+35.567483
+36.313160
+25.754159
+62.622885
+52.078601
+82.992087
+63.108076
+48.537387
+72.088146
+47.708756
+50.081352
+46.179143
+74.732584
+53.696995
+50.129993
+17.040583
+80.887178
+40.020833
+49.022050
+49.116439
+38.468226
+29.134830
+20.322282
+49.185777
+53.308382
+45.099085
+65.808325
+59.549146
+50.048213
+26.082749
+80.124302
+55.766722
+69.180818
+60.836923
+52.463229
+51.026135
+31.315524
+51.322238
+33.929750
+36.525866
+32.361278
+44.855573
+59.421811
+23.286046
+57.853846
+18.032623
+49.000570
+47.200617
+58.111273
+48.959961
+25.847692
+29.714310
+53.137056
+65.416045
+56.470946
+55.253781
+32.155232
+71.859925
+44.441666
+16.885794
+50.748223
+41.405682
+55.029351
+76.376410
+61.518971
+51.721628
+46.721816
+28.638947
+46.882807
+68.343571
+53.176561
+64.122778
+62.437319
+61.480298
+53.428447
+37.651474
+43.799034
+45.150540
+29.359705
+77.462318
+34.320945
+50.826392
+18.672423
+54.533843
+49.263052
+15.014251
+59.637263
+75.641556
+32.974664
+60.915148
+35.974519
+77.802002
+59.076702
+34.350295
+42.615288
+69.605218
+31.627390
+74.992208
+58.201044
+30.875197
+46.547036
+49.237101
+42.282544
+69.203356
+23.576466
+29.353965
+51.963650
+56.777796
+57.466679
+40.537154
+53.733623
+34.704655
+62.195681
+49.928415
+50.440171
+72.540199
+41.797528
+32.751826
+50.317731
+50.603325
+29.653995
+44.363277
+46.002078
+49.866360
+55.064603
+38.464424
+71.973447
+33.156272
+29.284836
+42.182426
+56.201244
+62.848672
+69.450503
+42.519988
+58.538124
+67.876770
+42.284114
+48.723362
+71.239238
+41.335381
+67.998167
+44.738949
+39.372789
+44.085337
+62.610914
+40.226752
+44.328863
+29.687844
+52.963598
+46.399305
+51.796664
+50.799966
+34.601864
+73.164871
+38.834143
+50.748055
+58.444272
+23.501147
+61.605060
+24.335268
+44.964741
+42.034866
+28.217985
+66.388532
+31.751391
+33.250285
+78.192329
+61.761701
+54.933711
+46.687613
+13.441307
+58.399611
+48.789001
+54.413686
+47.798646
+60.974053
+46.095188
+77.736080
+45.382836
+63.210533
+82.218378
+29.634936
+44.717552
+57.165995
+54.695814
+46.757029
+30.994554
+55.775549
+34.215764
+81.310734
+59.001417
+46.079728
+42.117032
+48.162080
+57.650783
+44.735961
+59.745161
+55.039142
+52.170244
+30.148709
+36.066474
+54.716652
+24.967065
+50.843673
+62.297811
+49.496099
+23.585305
+51.888732
+46.313279
+55.850779
+22.393465
+56.058621
+52.717924
+77.662074
+34.000533
+14.115106
+75.600210
+36.806491
+52.840479
+25.554121
+18.299383
+39.884859
+74.274848
+57.681610
+48.870748
+56.811627
+40.323529
+64.027898
+54.749657
+66.107093
+72.303001
+60.942526
+54.115156
+64.309181
+42.753524
+61.962672
+56.998966
+66.032093
+74.258508
+39.864467
+45.187562
+47.024809
+78.548947
+51.666372
+80.538611
+59.184048
+49.583706
+37.009837
+47.267822
+48.440376
+68.307612
+51.023075
+63.993605
+60.544180
+45.329090
+44.611970
+56.434869
+67.624087
+59.176585
+68.513906
+68.830402
+20.619566
+45.285990
+50.768093
+42.615570
+57.791240
+63.300958
+56.322222
+39.478805
+49.189127
+42.920404
+39.023948
+45.417217
+22.296066
+47.066346
+55.762485
+60.253314
+37.568683
+67.782594
+55.737468
+71.387626
+46.630654
+56.758652
+62.682231
+45.097253
+78.585691
+55.627721
+62.010825
+49.536678
+4.913428
+60.516656
+60.876080
+32.450371
+39.049506
+37.752071
+57.404212
+53.598622
+49.306831
+41.504588
+48.036989
+56.673481
+44.928617
+56.359062
+60.992957
+59.033875
+51.883007
+30.652988
+48.403692
+93.075022
+37.637492
+36.185365
+46.091212
+46.387284
+59.591843
+53.479518
+55.205289
+39.053466
+40.187032
+56.556575
+21.922778
+40.453022
+54.711698
+34.355186
+48.573944
+52.363719
+46.941065
+39.294103
+33.816825
+44.250689
+44.074156
+48.947397
+61.858121
+46.581662
+34.903942
+49.315023
+65.599510
+39.496400
+47.746650
+25.082062
+39.310162
+49.861966
+60.633814
+71.293685
+58.461712
+43.419262
+58.911596
+31.065021
+62.432397
+61.965042
+57.238112
+48.540426
+41.931047
+49.954690
+33.390882
+62.522379
+57.253377
+74.839880
+66.559072
+30.993192
+70.112733
+43.431678
+74.371371
+67.418406
+51.656030
+41.598203
+48.328989
+28.741102
+33.778325
+67.070264
+48.586437
+42.871144
+70.542905
+31.149471
+32.989862
+49.935477
+58.544938
+67.995866
+41.084719
+62.600805
+63.003809
+43.959093
+95.039498
+51.635094
+42.594618
+56.738454
+56.472886
+72.454830
+54.390798
+65.135740
+70.138773
+45.275571
+54.464354
+28.263000
+63.981719
+41.848561
+55.615102
+35.448199
+86.911426
+44.242514
+32.677179
+40.452974
+34.386452
+52.977132
+64.966342
+39.537276
+57.530906
+54.345038
+55.536818
+55.999242
+45.167076
+40.372522
+22.215040
+45.366335
+49.567678
+48.779479
+30.159274
+56.561762
+68.434903
+36.236297
+35.488041
+77.472220
+38.989784
+39.402822
+68.317668
+75.229367
+53.419890
+60.173582
+26.209845
+48.357315
+29.727833
+38.147947
+67.890142
+22.794397
+31.554084
+58.424533
+46.306834
+59.655932
+55.330720
+54.258171
+31.582894
+41.312617
+73.765279
+53.500950
+74.922643
+46.323867
+53.648006
+37.480867
+61.356103
+27.769268
+39.382548
+44.185602
+66.040173
+56.410287
+37.092155
+68.530676
+51.842190
+41.236812
+40.983752
+27.691441
+31.891113
+59.483029
+66.877746
+74.394752
+43.754073
+61.243756
+60.027122
+39.725852
+45.948957
+57.284519
+45.996091
+67.530106
+47.148547
+32.494688
+29.333068
+54.995925
+34.525909
+63.324913
+54.005796
+36.665937
+55.685400
+55.079378
+51.315077
+24.376215
+61.887355
+47.105497
+46.901127
+31.950832
+51.792501
+57.443122
+43.485227
+30.458080
+66.059519
+29.969853
+67.121573
+41.071706
+66.490999
+47.524504
+35.631804
+80.569670
+69.667320
+31.954822
+36.904120
+50.375188
+19.774263
+55.692532
+68.069211
+43.978549
+46.565912
+33.415154
+54.959587
+41.498255
+45.510471
+53.768895
+47.423433
+36.227767
+60.372391
+56.602051
+11.669908
+59.133000
+54.510422
+44.251599
+38.670563
+57.824793
+48.460889
+53.916399
+60.547234
+57.513630
+32.481570
+44.472237
+47.860284
+60.360647
+61.895478
+44.809410
+46.069994
+50.202907
+46.490782
+77.183441
+45.670381
+69.002411
+29.191174
+52.991669
+25.541652
+12.082276
+44.325765
+49.446058
+51.843428
+71.070566
+81.170712
+42.853130
+48.259251
--- a/runs/DevcontainerResult/run.cwl
+++ b/runs/DevcontainerResult/run.cwl
+cwlVersion: v1.2
+class: Workflow
+
+requirements:
+  MultipleInputFeatureRequirement: {}
+
+inputs:
+  arcDirectory: Directory
+
+steps:
+  Devcontainer:
+    run: ../../workflows/Devcontainer/workflow.cwl
+    in:
+      arcDirectory: arcDirectory
+    out: [output]
+
+outputs:
+  DevcontainerResult:
+    type: File
+    outputSource: Devcontainer/output
\ No newline at end of file
--- a/runs/DevcontainerResult/run.yml
+++ b/runs/DevcontainerResult/run.yml
+arcDirectory:
+  class: Directory
+  path: ../../
+
+arc:performer:
+  - class: arc:Person
+    arc:first name: "Caroline"
+    arc:last name: "Ott"
+    arc:email: "ottj@rptu.de"
+    arc:affiliation: "RPTU Kaiserslautern/Landau"
+
+$namespaces:
+  arc: https://github.com/nfdi4plants/ARC_ontology
+
+$schemas:
+  - https://raw.githubusercontent.com/nfdi4plants/ARC_ontology/main/ARC_v2.0.owl
--- a/runs/FixedScriptResult/result.csv
+++ b/runs/FixedScriptResult/result.csv
+Sum_1-2
+52.374927
+30.708113
+43.347295
+32.330910
+68.832634
+50.943254
+82.709457
+45.815823
+49.329293
+15.044567
+42.581675
+61.490285
+61.483285
+33.515325
+39.027573
+57.814962
+41.484288
+62.969456
+56.084297
+76.014723
+39.715133
+73.319637
+67.026630
+56.888570
+48.411011
+70.181930
+18.055983
+35.218257
+26.840155
+72.385753
+43.972671
+44.078586
+53.938409
+43.395488
+28.723837
+54.061480
+58.528494
+52.236839
+56.893014
+56.525366
+58.955729
+46.444395
+39.269410
+44.423325
+19.510763
+48.672524
+64.933334
+60.750569
+45.516685
+46.623334
+76.270554
+29.934011
+50.275506
+40.572500
+55.508817
+43.844585
+57.298854
+38.721723
+49.707433
+48.383707
+73.873611
+56.579798
+49.573657
+74.940937
+48.889656
+11.609634
+39.675693
+29.804500
+43.964936
+35.057027
+37.625311
+77.481503
+41.714170
+52.904955
+35.366910
+39.166247
+53.024085
+7.132227
+54.059714
+38.487312
+79.778612
+49.592970
+42.861946
+63.583801
+81.084601
+29.562834
+54.967924
+56.813437
+50.634788
+45.835761
+53.669806
+27.804082
+62.293055
+42.933661
+34.954878
+64.885836
+57.539051
+33.539328
+69.979137
+28.013399
+35.567483
+36.313160
+25.754159
+62.622885
+52.078601
+82.992087
+63.108076
+48.537387
+72.088146
+47.708756
+50.081352
+46.179143
+74.732584
+53.696995
+50.129993
+17.040583
+80.887178
+40.020833
+49.022050
+49.116439
+38.468226
+29.134830
+20.322282
+49.185777
+53.308382
+45.099085
+65.808325
+59.549146
+50.048213
+26.082749
+80.124302
+55.766722
+69.180818
+60.836923
+52.463229
+51.026135
+31.315524
+51.322238
+33.929750
+36.525866
+32.361278
+44.855573
+59.421811
+23.286046
+57.853846
+18.032623
+49.000570
+47.200617
+58.111273
+48.959961
+25.847692
+29.714310
+53.137056
+65.416045
+56.470946
+55.253781
+32.155232
+71.859925
+44.441666
+16.885794
+50.748223
+41.405682
+55.029351
+76.376410
+61.518971
+51.721628
+46.721816
+28.638947
+46.882807
+68.343571
+53.176561
+64.122778
+62.437319
+61.480298
+53.428447
+37.651474
+43.799034
+45.150540
+29.359705
+77.462318
+34.320945
+50.826392
+18.672423
+54.533843
+49.263052
+15.014251
+59.637263
+75.641556
+32.974664
+60.915148
+35.974519
+77.802002
+59.076702
+34.350295
+42.615288
+69.605218
+31.627390
+74.992208
+58.201044
+30.875197
+46.547036
+49.237101
+42.282544
+69.203356
+23.576466
+29.353965
+51.963650
+56.777796
+57.466679
+40.537154
+53.733623
+34.704655
+62.195681
+49.928415
+50.440171
+72.540199
+41.797528
+32.751826
+50.317731
+50.603325
+29.653995
+44.363277
+46.002078
+49.866360
+55.064603
+38.464424
+71.973447
+33.156272
+29.284836
+42.182426
+56.201244
+62.848672
+69.450503
+42.519988
+58.538124
+67.876770
+42.284114
+48.723362
+71.239238
+41.335381
+67.998167
+44.738949
+39.372789
+44.085337
+62.610914
+40.226752
+44.328863
+29.687844
+52.963598
+46.399305
+51.796664
+50.799966
+34.601864
+73.164871
+38.834143
+50.748055
+58.444272
+23.501147
+61.605060
+24.335268
+44.964741
+42.034866
+28.217985
+66.388532
+31.751391
+33.250285
+78.192329
+61.761701
+54.933711
+46.687613
+13.441307
+58.399611
+48.789001
+54.413686
+47.798646
+60.974053
+46.095188
+77.736080
+45.382836
+63.210533
+82.218378
+29.634936
+44.717552
+57.165995
+54.695814
+46.757029
+30.994554
+55.775549
+34.215764
+81.310734
+59.001417
+46.079728
+42.117032
+48.162080
+57.650783
+44.735961
+59.745161
+55.039142
+52.170244
+30.148709
+36.066474
+54.716652
+24.967065
+50.843673
+62.297811
+49.496099
+23.585305
+51.888732
+46.313279
+55.850779
+22.393465
+56.058621
+52.717924
+77.662074
+34.000533
+14.115106
+75.600210
+36.806491
+52.840479
+25.554121
+18.299383
+39.884859
+74.274848
+57.681610
+48.870748
+56.811627
+40.323529
+64.027898
+54.749657
+66.107093
+72.303001
+60.942526
+54.115156
+64.309181
+42.753524
+61.962672
+56.998966
+66.032093
+74.258508
+39.864467
+45.187562
+47.024809
+78.548947
+51.666372
+80.538611
+59.184048
+49.583706
+37.009837
+47.267822
+48.440376
+68.307612
+51.023075
+63.993605
+60.544180
+45.329090
+44.611970
+56.434869
+67.624087
+59.176585
+68.513906
+68.830402
+20.619566
+45.285990
+50.768093
+42.615570
+57.791240
+63.300958
+56.322222
+39.478805
+49.189127
+42.920404
+39.023948
+45.417217
+22.296066
+47.066346
+55.762485
+60.253314
+37.568683
+67.782594
+55.737468
+71.387626
+46.630654
+56.758652
+62.682231
+45.097253
+78.585691
+55.627721
+62.010825
+49.536678
+4.913428
+60.516656
+60.876080
+32.450371
+39.049506
+37.752071
+57.404212
+53.598622
+49.306831
+41.504588
+48.036989
+56.673481
+44.928617
+56.359062
+60.992957
+59.033875
+51.883007
+30.652988
+48.403692
+93.075022
+37.637492
+36.185365
+46.091212
+46.387284
+59.591843
+53.479518
+55.205289
+39.053466
+40.187032
+56.556575
+21.922778
+40.453022
+54.711698
+34.355186
+48.573944
+52.363719
+46.941065
+39.294103
+33.816825
+44.250689
+44.074156
+48.947397
+61.858121
+46.581662
+34.903942
+49.315023
+65.599510
+39.496400
+47.746650
+25.082062
+39.310162
+49.861966
+60.633814
+71.293685
+58.461712
+43.419262
+58.911596
+31.065021
+62.432397
+61.965042
+57.238112
+48.540426
+41.931047
+49.954690
+33.390882
+62.522379
+57.253377
+74.839880
+66.559072
+30.993192
+70.112733
+43.431678
+74.371371
+67.418406
+51.656030
+41.598203
+48.328989
+28.741102
+33.778325
+67.070264
+48.586437
+42.871144
+70.542905
+31.149471
+32.989862
+49.935477
+58.544938
+67.995866
+41.084719
+62.600805
+63.003809
+43.959093
+95.039498
+51.635094
+42.594618
+56.738454
+56.472886
+72.454830
+54.390798
+65.135740
+70.138773
+45.275571
+54.464354
+28.263000
+63.981719
+41.848561
+55.615102
+35.448199
+86.911426
+44.242514
+32.677179
+40.452974
+34.386452
+52.977132
+64.966342
+39.537276
+57.530906
+54.345038
+55.536818
+55.999242
+45.167076
+40.372522
+22.215040
+45.366335
+49.567678
+48.779479
+30.159274
+56.561762
+68.434903
+36.236297
+35.488041
+77.472220
+38.989784
+39.402822
+68.317668
+75.229367
+53.419890
+60.173582
+26.209845
+48.357315
+29.727833
+38.147947
+67.890142
+22.794397
+31.554084
+58.424533
+46.306834
+59.655932
+55.330720
+54.258171
+31.582894
+41.312617
+73.765279
+53.500950
+74.922643
+46.323867
+53.648006
+37.480867
+61.356103
+27.769268
+39.382548
+44.185602
+66.040173
+56.410287
+37.092155
+68.530676
+51.842190
+41.236812
+40.983752
+27.691441
+31.891113
+59.483029
+66.877746
+74.394752
+43.754073
+61.243756
+60.027122
+39.725852
+45.948957
+57.284519
+45.996091
+67.530106
+47.148547
+32.494688
+29.333068
+54.995925
+34.525909
+63.324913
+54.005796
+36.665937
+55.685400
+55.079378
+51.315077
+24.376215
+61.887355
+47.105497
+46.901127
+31.950832
+51.792501
+57.443122
+43.485227
+30.458080
+66.059519
+29.969853
+67.121573
+41.071706
+66.490999
+47.524504
+35.631804
+80.569670
+69.667320
+31.954822
+36.904120
+50.375188
+19.774263
+55.692532
+68.069211
+43.978549
+46.565912
+33.415154
+54.959587
+41.498255
+45.510471
+53.768895
+47.423433
+36.227767
+60.372391
+56.602051
+11.669908
+59.133000
+54.510422
+44.251599
+38.670563
+57.824793
+48.460889
+53.916399
+60.547234
+57.513630
+32.481570
+44.472237
+47.860284
+60.360647
+61.895478
+44.809410
+46.069994
+50.202907
+46.490782
+77.183441
+45.670381
+69.002411
+29.191174
+52.991669
+25.541652
+12.082276
+44.325765
+49.446058
+51.843428
+71.070566
+81.170712
+42.853130
+48.259251
--- a/runs/FixedScriptResult/run.cwl
+++ b/runs/FixedScriptResult/run.cwl
+cwlVersion: v1.2
+class: Workflow
+
+requirements:
+  MultipleInputFeatureRequirement: {}
+
+inputs:
+  firstArg: File
+  secondArg: string
+
+steps:
+  FixedScript:
+    run: ../../workflows/FixedScript/workflow.cwl
+    in:
+      firstArg: firstArg
+      secondArg: secondArg
+    out: [output]
+
+outputs:
+  FixedScriptResult:
+    type: File
+    outputSource: FixedScript/output
\ No newline at end of file
--- a/runs/FSharpArcCapsule.yml
+++ b/runs/FSharpArcCapsule.yml
-arcDirectory:
-  class: Directory
-  path: ../
 firstArg:
  class: File
-  path: ../assays/measurement1/dataset/table.csv
+  path: ../../assays/measurement1/dataset/proteomics_result.csv
 secondArg: ./result.csv

+arc:performer:
+  - class: arc:Person
+    arc:first name: "Caroline"
+    arc:last name: "Ott"
+    arc:email: "caroline.ott@rptu.de"
+    arc:affiliation: "Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau"
+
 arc:has process sequence:
-  - class: arc:process sequence
+  - class: arc:process
    arc:has input: 
      - class: arc:data
        arc:name: "./arc/assays/measurement1/dataset/table.csv"
    arc:has output:
      - class: arc:data
-        arc:name: "./arc/runs/fsResult1/result.csv"
+        arc:name: "./arc/runs/ARCMountResult/result.csv"

 $namespaces:
  arc: https://github.com/nfdi4plants/ARC_ontology

--- a/runs/README.md
+++ b/runs/README.md
 # CWL examples

 :bulb: Requires installation of a CWL runner and docker  
-&rarr; checkout CWL guides in the [DataPLANT Knowledge Base](https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/guides/ComputationalWorkflows/index.html)
+&rarr; checkout CWL guides in the [DataPLANT Knowledge Base](https://nfdi4plants.github.io/nfdi4plants.knowledgebase/guides/arc-cwl/)

-All three workflow examples below (re)create the file [fsResult1/result.csv](fsResult1/result.csv).
+All three workflow examples below (re)create the file [*/result.csv](ARCMountResult/result.csv).

-## with a docker container
+## with a docker container and a fixed script

 ```bash
-cd runs/fsResult1
-cwltool ../../workflows/FixedScript/FSharpArcCapsule.cwl ../FSharpArcCapsule.yml
+cd runs/FixedScriptResult
+cwltool run.cwl run.yml
 ```

 ## With a fixed script in a mounted arc

 ```bash
-cd runs/fsResult1
-cwltool ../../workflows/ARCMount/FSharpArcCapsule.cwl ../FSharpArcCapsule.yml
+cd runs/ARCMountResult
+cwltool run.cwl run.yml
 ```

 ## Within an ARC with a devcontainer

 ```bash
-cd runs/fsResult1
-cwltool ../../workflows/Devcontainer/FSharpArcCapsule.cwl ../FSharpArcCapsule.yml
+cd runs/DevContainerResult
+cwltool run.cwl run.yml
 ```
--- a/studies/experiment1_material/README.md
+++ b/studies/experiment1_material/README.md
--- a/studies/MaterialPreparation/isa.study.xlsx
+++ b/studies/MaterialPreparation/isa.study.xlsx
--- a/studies/experiment1_material/isa.study_unnecessarilyFilled.xlsx
+++ b/studies/experiment1_material/isa.study_unnecessarilyFilled.xlsx
--- a/studies/experiment1_material/protocols/.gitkeep
+++ b/studies/experiment1_material/protocols/.gitkeep
--- a/studies/experiment1_material/resources/.gitkeep
+++ b/studies/experiment1_material/resources/.gitkeep
--- a/studies/experiment1_material/resources/Sample1_e36ca6b8-19ba-4504-aa82-d4781765873d.png
+++ b/studies/experiment1_material/resources/Sample1_e36ca6b8-19ba-4504-aa82-d4781765873d.png
No results found