- name: picard collectmultiplemetrics test_picard_collectmultiplemetrics
  command: nextflow run ./tests/modules/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics -c ./tests/config/nextflow.config  -c ./tests/modules/picard/collectmultiplemetrics/nextflow.config
  tags:
    - picard
    - picard/collectmultiplemetrics
  files:
    - path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
      contains:
        - "## METRICS CLASS\tpicard.analysis.AlignmentSummaryMetrics"
    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
      contains:
        - "READ_END\tCYCLE\tPCT_A\tPCT_C\tPCT_G\tPCT_T\tPCT_N"
        - "1\t1\t20\t26\t32\t22\t0"
    - path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
    - path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
      contains:
        - "MEDIAN_INSERT_SIZE\tMODE_INSERT_SIZE\tMEDIAN_ABSOLUTE_DEVIATION\tMIN_INSERT_SIZE\tMAX_INSERT_SIZE\tMEAN_INSERT_SIZE\tSTANDARD_DEVIATION\tREAD_PAIRS\tPAIR_ORIENTATION\tWIDTH_OF_10_PERCENT\tWIDTH_OF_20_PERCENT\tWIDTH_OF_30_PERCENT\tWIDTH_OF_40_PERCENT\tWIDTH_OF_50_PERCENT\tWIDTH_OF_60_PERCENT\tWIDTH_OF_70_PERCENT\tWIDTH_OF_80_PERCENT\tWIDTH_OF_90_PERCENT\tWIDTH_OF_95_PERCENT\tWIDTH_OF_99_PERCENT\tSAMPLE\tLIBRARY\tREAD_GROUP"
        - "209\t159\t46\t77\t364\t207.659794\t66.769018\t97\tFR\t25\t49\t59\t77\t93\t123\t145\t183\t223\t255\t311"
    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
      contains:
        - "CYCLE\tMEAN_QUALITY"
        - "1\t32"
        - "2\t31.35"
    - path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
    - path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
      contains:
        - "QUALITY\tCOUNT_OF_Q"
        - "14\t1926"
    - path: output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf

- name: picard collectmultiplemetrics test_picard_collectmultiplemetrics_nofasta
  command: nextflow run ./tests/modules/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics_nofasta -c ./tests/config/nextflow.config  -c ./tests/modules/picard/collectmultiplemetrics/nextflow.config
  tags:
    - picard
    - picard/collectmultiplemetrics
  files:
    - path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
      contains:
        - "## METRICS CLASS\tpicard.analysis.AlignmentSummaryMetrics"
    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
      contains:
        - "READ_END\tCYCLE\tPCT_A\tPCT_C\tPCT_G\tPCT_T\tPCT_N"
        - "1\t1\t20\t26\t32\t22\t0"
    - path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
    - path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
      contains:
        - "MEDIAN_INSERT_SIZE\tMODE_INSERT_SIZE\tMEDIAN_ABSOLUTE_DEVIATION\tMIN_INSERT_SIZE\tMAX_INSERT_SIZE\tMEAN_INSERT_SIZE\tSTANDARD_DEVIATION\tREAD_PAIRS\tPAIR_ORIENTATION\tWIDTH_OF_10_PERCENT\tWIDTH_OF_20_PERCENT\tWIDTH_OF_30_PERCENT\tWIDTH_OF_40_PERCENT\tWIDTH_OF_50_PERCENT\tWIDTH_OF_60_PERCENT\tWIDTH_OF_70_PERCENT\tWIDTH_OF_80_PERCENT\tWIDTH_OF_90_PERCENT\tWIDTH_OF_95_PERCENT\tWIDTH_OF_99_PERCENT\tSAMPLE\tLIBRARY\tREAD_GROUP"
        - "209\t159\t46\t77\t364\t207.659794\t66.769018\t97\tFR\t25\t49\t59\t77\t93\t123\t145\t183\t223\t255\t311"
    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
      contains:
        - "CYCLE\tMEAN_QUALITY"
        - "1\t32"
        - "2\t31.35"
    - path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
    - path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
      contains:
        - "QUALITY\tCOUNT_OF_Q"
        - "14\t1926"
    - path: output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf

- name: picard collectmultiplemetrics test_picard_collectmultiplemetrics_cram
  command: nextflow run ./tests/modules/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics_cram -c ./tests/config/nextflow.config  -c ./tests/modules/picard/collectmultiplemetrics/nextflow.config
  tags:
    - picard
    - picard/collectmultiplemetrics
  files:
    - path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
      contains:
        - "## METRICS CLASS\tpicard.analysis.AlignmentSummaryMetrics"
    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
      contains:
        - "READ_END\tCYCLE\tPCT_A\tPCT_C\tPCT_G\tPCT_T\tPCT_N"
        - "1\t1\t34.065934\t15.242822\t16.093584\t34.526764\t0.070897"
    - path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
    - path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
      contains:
        - "MEDIAN_INSERT_SIZE\tMODE_INSERT_SIZE\tMEDIAN_ABSOLUTE_DEVIATION\tMIN_INSERT_SIZE\tMAX_INSERT_SIZE\tMEAN_INSERT_SIZE\tSTANDARD_DEVIATION\tREAD_PAIRS\tPAIR_ORIENTATION\tWIDTH_OF_10_PERCENT\tWIDTH_OF_20_PERCENT\tWIDTH_OF_30_PERCENT\tWIDTH_OF_40_PERCENT\tWIDTH_OF_50_PERCENT\tWIDTH_OF_60_PERCENT\tWIDTH_OF_70_PERCENT\tWIDTH_OF_80_PERCENT\tWIDTH_OF_90_PERCENT\tWIDTH_OF_95_PERCENT\tWIDTH_OF_99_PERCENT\tSAMPLE\tLIBRARY\tREAD_GROUP"
        - "123\t96\t23\t32\t300\t125.684397\t32.447863\t2820\tFR\t11\t17\t27\t37\t47\t57\t69\t83\t103\t125\t169"
    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
      contains:
        - "CYCLE\tMEAN_QUALITY"
        - "1\t41.018079"
        - "2\t40.981921"
    - path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
    - path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
      contains:
        - "QUALITY\tCOUNT_OF_Q"
        - "3\t2"
        - "4\t44"
    - path: output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf