Updated samplesheet processing and testing to new scheme

                print_error("Control entry and sample entry must be different!", "Line", line)

            ## Check replicate entry is integer

            if not replicate.isdigit() & int(replicate) > 0:

                print_error("Replicate id not an integer or is not > 0!", "Line", line)

            if not replicate.isdigit():

                print_error("Replicate id not an integer", "Line", line)

            replicate = int(replicate)

            if replicate <= 0:

                print_error("Replicate must be > 0", "Line", line)

            ## Check FastQ file extension

            for fastq in [fastq_1, fastq_2]:

    ## Create control identity variable

    for sample in sorted(sample_run_dict.keys()):

        for replicate in sorted(sample_run_dict[sample].keys()):

            sample_info = sample_run_dict[sample][replicate][0]

            for idx, sample_info in enumerate(sample_run_dict[sample][replicate]):

                if control_present:

                    if sample_info[0] in control_names_list:

                        sample_info.append("1")

                        sample_info.append("0")

                else: 

                    sample_info.append("0")

            sample_run_dict[sample][replicate][0] = sample_info

    ## Check igg_control parameter is consistent with input groups

    if (use_control == 'true' and not control_present):

        print_error("ERROR: No 'control' group was found in " + str(file_in) + " If you are not supplying a control, please specify --igg_control 'false' on command line.")

        print_error("ERROR: No 'control' group was found in " + str(file_in) + " If you are not supplying a control, please specify --use_control 'false' on command line.")

    if (use_control == 'false' and control_present):

        print("WARNING: Parameter --igg_control was set to false, but an 'igg' group was found in " + str(file_in) + ".")

        print("WARNING: Parameter --use_control was set to false, but an control group was found in " + str(file_in) + ".")

    ## Write validated samplesheet with appropriate columns

    if len(sample_run_dict) > 0:

                uniq_rep_ids = set(sample_run_dict[sample].keys())

                if len(uniq_rep_ids) != max(uniq_rep_ids):

                    print_error(

                        "Replicate ids must start with 1..<num_replicates>!",

                        "Replicate ids must start with 1!",

                        "Group",

                        sample,

                    )

    - test_samplesheet

  exit_code: 1

# Test dot in group id

- name: test_samplesheet_check_group_name_with_dot

  command: nextflow run main.nf -profile docker,test --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/unit_tests/sample_dot.csv -c tests/config/nextflow.config

  tags:

    - test_samplesheet

  files:

    - path: results/pipeline_info/samplesheet.valid.csv

# Test invalid number of columns in row

- name: test_samplesheet_invalid_cols_in_row

  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/unit_tests/invalid_column_in_row.csv -c tests/config/nextflow.config

  tags:

    - test_samplesheet

  exit_code: 1

# - name: test_samplesheet_check_1_1_pos

#   command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/unit_tests/single_sample_single_igg.csv -c tests/config/nextflow.config

#   tags:

#     - samplesheet

#     - samplesheet_1_1

#     - samplesheet_1_1_pos

#   files:

#     - path: results/pipeline_info/samplesheet.valid.csv

# - name: test_samplesheet_check_1_1_neg

#   command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/unit_tests/single_sample_single_igg_neg.csv -c tests/config/nextflow.config

#   tags:

#     - samplesheet

#     - samplesheet_1_1

#     - samplesheet_1_1_neg

#   exit_code: 1

# Test group is blank

- name: test_samplesheet_group_is_blank

  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/unit_tests/group_is_blank.csv -c tests/config/nextflow.config

  tags:

    - test_samplesheet

  exit_code: 1

# - name: test_samplesheet_check_1_2_group_match

#   command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/unit_tests/single_sample_single_igg_non_matching_groups.csv -c tests/config/nextflow.config

#   tags:

#     - samplesheet

#     - samplesheet_1_2

#     - samplesheet_1_2_group_match

#   exit_code: 1

# Test group has spaces

- name: test_samplesheet_group_has_spaces

  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/unit_tests/group_has_spaces.csv -c tests/config/nextflow.config

  tags:

    - test_samplesheet

  exit_code: 1

# - name: test_samplesheet_check_2_2_group_match_tech_rep

#   command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/unit_tests/single_sample_single_igg_non_matching_groups_tech_rep.csv -c tests/config/nextflow.config

#   tags:

#     - samplesheet

#     - samplesheet_2_2

#     - samplesheet-2_2_group_match_tech_rep

#   exit_code: 1

# Test control has spaces

- name: test_samplesheet_control_has_spaces

  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/unit_tests/control_has_spaces.csv -c tests/config/nextflow.config

  tags:

    - test_samplesheet

  exit_code: 1

# - name: test_samplesheet_check_multiple_sample_single_igg

#   command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/unit_tests/multiple_sample_single_igg.csv -c tests/config/nextflow.config

#   tags:

#     - samplesheet

#     - samplesheet_M_1

#   files:

#     - path: results/pipeline_info/samplesheet.valid.csv

# Test group equals control

- name: test_samplesheet_group_equals_control

  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/unit_tests/group_equals_control.csv -c tests/config/nextflow.config

  tags:

    - test_samplesheet

  exit_code: 1

# - name: test_samplesheet_check_multiple_sample_multiple_igg

#   command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/unit_tests/multiple_sample_multiple_igg.csv -c tests/config/nextflow.config

#   tags:

#     - samplesheet

#     - samplesheet_M_M

#   files:

#     - path: results/pipeline_info/samplesheet.valid.csv

# Test negative replicate number

- name: test_samplesheet_neg_rep

  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/unit_tests/negative_rep_num.csv -c tests/config/nextflow.config

  tags:

    - test_samplesheet

  exit_code: 1

# - name: test_samplesheet_check_group_name_with_dot

#   command: nextflow run main.nf -profile docker,test --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/test-GSE145187-small-dot.csv -c tests/config/nextflow.config

#   tags:

#     - samplesheet_group_dot

#   files:

#     - path: results/pipeline_info/samplesheet.valid.csv

# Test replicate number does not start at 1

- name: test_samplesheet_rep_not_start_one

  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/unit_tests/rep_not_start_one.csv -c tests/config/nextflow.config

  tags:

    - test_samplesheet

  exit_code: 1

# Test fastq ext incorrect

- name: test_samplesheet_fastq_ext_error

  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/unit_tests/fastq_ext_error.csv -c tests/config/nextflow.config

  tags:

    - test_samplesheet

  exit_code: 1

# Test fastq path spaces

- name: test_samplesheet_fastq_path_spaces_error

  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/unit_tests/fastq_file_spaces.csv -c tests/config/nextflow.config

  tags:

    - test_samplesheet

  exit_code: 1

# Test duplicate rows

- name: test_samplesheet_dup_rows

  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/unit_tests/duplicate_rows.csv -c tests/config/nextflow.config

  tags:

    - test_samplesheet

  exit_code: 1

# Test control not exist

- name: test_samplesheet_ctrl_not_exist

  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/unit_tests/control_not_exist.csv -c tests/config/nextflow.config

  tags:

    - test_samplesheet

  exit_code: 1

# Test control with control

- name: test_samplesheet_ctrl_with_ctrl

  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/unit_tests/control_with_control.csv -c tests/config/nextflow.config

  tags:

    - test_samplesheet

  exit_code: 1

# Test small sample sheet

- name: test_samplesheet_small

  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/test-GSE145187-small.csv -c tests/config/nextflow.config

  tags:

    - test_samplesheet

  files:

    - path: results/pipeline_info/samplesheet.valid.csv

# Test small tech reps

- name: test_samplesheet_small_tech_reps

  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/test-GSE145187-small-tech-reps.csv -c tests/config/nextflow.config

  tags:

    - test_samplesheet

  files:

    - path: results/pipeline_info/samplesheet.valid.csv

# Test noigg small

- name: test_samplesheet_small_noigg

  command: nextflow run main.nf -profile docker,test --only_input true --use_control false --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/test-GSE145187-noigg-small.csv -c tests/config/nextflow.config

  tags:

    - test_samplesheet

  files:

    - path: results/pipeline_info/samplesheet.valid.csv

# Test all

- name: test_samplesheet_all

  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/test-GSE145187-all.csv -c tests/config/nextflow.config

  tags:

    - test_samplesheet

  files:

    - path: results/pipeline_info/samplesheet.valid.csv

# Test all small

- name: test_samplesheet_all_small

  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/test-GSE145187-all-small.csv -c tests/config/nextflow.config

  tags:

    - test_samplesheet

  files:

    - path: results/pipeline_info/samplesheet.valid.csv

# - name: test_samplesheet_check_test_id_1

#   command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/unit_tests/rep_id_start_1.csv -c tests/config/nextflow.config

#   tags:

#     - samplesheet

#     - samplesheet_start_1

#   exit_code: 1

 No newline at end of file

# Test all multi-rep

- name: test_samplesheet_all_multi_rep

  command: nextflow run main.nf -profile docker,test --only_input true --input https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/test-GSE145187-all-multi-rep.csv -c tests/config/nextflow.config

  tags:

    - test_samplesheet

  files:

    - path: results/pipeline_info/samplesheet.valid.csv